pax_global_header00006660000000000000000000000064127620157350014522gustar00rootroot0000000000000052 comment=fd6c7fa704eef19a5b950835f714542ab31aeda6 Fastaq-3.14.0/000077500000000000000000000000001276201573500130265ustar00rootroot00000000000000Fastaq-3.14.0/.gitignore000066400000000000000000000004571276201573500150240ustar00rootroot00000000000000*.py[cod] # C extensions *.so # Packages *.egg *.egg-info dist build eggs parts bin var sdist develop-eggs .installed.cfg lib lib64 # Installer logs pip-log.txt # Unit test / coverage reports .coverage .tox nosetests.xml # Translations *.mo # Mr Developer .mr.developer.cfg .project .pydevproject Fastaq-3.14.0/.travis.yml000066400000000000000000000001221276201573500151320ustar00rootroot00000000000000language: python python: - "3.4" sudo: false script: - "python setup.py test" Fastaq-3.14.0/AUTHORS000066400000000000000000000000401276201573500140700ustar00rootroot00000000000000Martin Hunt (mh12@sanger.ac.uk) Fastaq-3.14.0/LICENSE000066400000000000000000001045241276201573500140410ustar00rootroot00000000000000GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. {http://fsf.org/} Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. {one line to give the program's name and a brief idea of what it does.} Copyright (C) {year} {name of author} This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see {http://www.gnu.org/licenses/}. Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Fastaq Copyright (C) 2013 Pathogen Genomics, Wellcome Trust Sanger Institute This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see {http://www.gnu.org/licenses/}. The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read {http://www.gnu.org/philosophy/why-not-lgpl.html}. Fastaq-3.14.0/MANIFEST.in000066400000000000000000000000651276201573500145650ustar00rootroot00000000000000recursive-include pyfastaq/tests *.txt *.py *_test_* Fastaq-3.14.0/README.md000066400000000000000000000136651276201573500143200ustar00rootroot00000000000000Fastaq ====== Python3 script to manipulate FASTA and FASTQ (and other format) files, plus API for developers Installation ------------ Install with pip3: pip3 install pyfastaq Alternatively, you can download the latest release from this github repository, or clone the repository. Then run the tests: python3 setup.py test If the tests all pass, install: python3 setup.py install Usage ----- The installation will put a single script called `fastaq` in your path. The usage is: fastaq [options] Key points: * To list the available commands and brief descriptions, just run `fastaq` * Use `fastaq command -h` or `fastaq command --help` to get a longer description and the usage of that command. * The type of input file is automatically detected. Currently supported: `FASTA`, `FASTQ`, `GFF3`, `EMBL`, `GBK`, `Phylip`. * `fastaq` only manipulates sequences (and quality scores if present), so annotation is ignored where present in the input. * Input and output files can be gzipped. An input file is assumed to be gzipped if its name ends with .gz. To gzip an output file, just name it with .gz at the end. * You can use a minus sign for a filename to use stdin or stdout, so commands can be piped together. See the example below. Examples -------- Reverse complement all sequences in a file: fastaq reverse_complement in.fastq out.fastq Reverse complement all sequences in a gzipped file, then translate each sequence: fastaq reverse_complement in.fastq.gz - | fastaq translate - out.fasta Available commands ------------------ | Command | Description | |-----------------------|----------------------------------------------------------------------| | acgtn_only | Replace every non acgtnACGTN with an N | | add_indels | Deletes or inserts bases at given position(s) | | caf_to_fastq | Converts a CAF file to FASTQ format | | capillary_to_pairs | Converts file of capillary reads to paired and unpaired files | | chunker | Splits sequences into equal sized chunks | | count_sequences | Counts the sequences in input file | | deinterleave | Splits interleaved paired file into two separate files | | enumerate_names | Renames sequences in a file, calling them 1,2,3... etc | | expand_nucleotides | Makes every combination of degenerate nucleotides | | fasta_to_fastq | Convert FASTA and .qual to FASTQ | | filter | Filter sequences to get a subset of them | | get_ids | Get the ID of each sequence | | get_seq_flanking_gaps | Gets the sequences flanking gaps | | interleave | Interleaves two files, output is alternating between fwd/rev reads | | make_random_contigs | Make contigs of random sequence | | merge | Converts multi sequence file to a single sequence | | replace_bases | Replaces all occurrences of one letter with another | | reverse_complement | Reverse complement all sequences | | scaffolds_to_contigs | Creates a file of contigs from a file of scaffolds | | search_for_seq | Find all exact matches to a string (and its reverse complement) | | sequence_trim | Trim exact matches to a given string off the start of every sequence | | sort_by_size | Sorts sequences in length order | | split_by_base_count | Split multi sequence file into separate files | | strip_illumina_suffix | Strips /1 or /2 off the end of every read name | | to_fake_qual | Make fake quality scores file | | to_fasta | Converts a variety of input formats to nicely formatted FASTA format | | to_mira_xml | Create an xml file from a file of reads, for use with Mira assembler | | to_orfs_gff | Writes a GFF file of open reading frames | | to_perfect_reads | Make perfect paired reads from reference | | to_random_subset | Make a random sample of sequences (and optionally mates as well) | | to_tiling_bam | Make a BAM file of reads uniformly spread across the input reference | | to_unique_by_id | Remove duplicate sequences, based on their names. Keep longest seqs | | translate | Translate all sequences in input nucleotide sequences | | trim_Ns_at_end | Trims all Ns at the start/end of all sequences | | trim_contigs | Trims a set number of bases off the end of every contig | | trim_ends | Trim fixed number of bases of start and/or end of every sequence | | version | Print version number and exit | For developers -------------- Here is a template for counting the sequences in a FASTA or FASTQ file: from pyfastaq import sequences seq_reader = sequences.file_reader(infile) count = 0 for seq in seq_reader: count += 1 print(count) Hopefully you get the idea and there are plenty of examples in tasks.py. Detection of the input file type and whether gzipped or not is automatic. See help(sequences) for the various methods already defined in the classes Fasta and Fastq. --------------------------------- Build status: [![Build Status](https://travis-ci.org/sanger-pathogens/Fastaq.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Fastaq) Fastaq-3.14.0/pyfastaq/000077500000000000000000000000001276201573500146565ustar00rootroot00000000000000Fastaq-3.14.0/pyfastaq/__init__.py000066400000000000000000000004341276201573500167700ustar00rootroot00000000000000from pkg_resources import get_distribution try: __version__ = get_distribution('pyfastaq').version except: __version__ = 'local' __all__ = [ 'caf', 'genetic_codes', 'utils', 'sequences', 'tasks', 'intervals', 'runners' ] from pyfastaq import * Fastaq-3.14.0/pyfastaq/caf.py000066400000000000000000000040521276201573500157620ustar00rootroot00000000000000from pyfastaq import sequences, utils class Error (Exception): pass def file_reader(fname): f = utils.open_file_read(fname) c = Caf() while c.get_next_from_file(f): yield c utils.close(f) class Caf: def __init__(self): self.id = None self.seq = None self.insert_min = None self.insert_max = None self.ligation = None self.clone = None self.clip_start = None self.clip_end = None def __eq__(self, other): if type(other) is type(self): return self.__dict__ == other.__dict__ return False def get_next_from_file(self, f): self.__init__() line = f.readline() if not line: return None while line == '\n': line = f.readline() if not line.startswith('DNA : '): raise Error("Error reading caf file. Expected line starting with 'DNA : ...'") self.id = line.rstrip().split()[2] line = f.readline() seq = [] while line != '\n': seq.append(line.rstrip()) line = f.readline() self.seq = sequences.Fasta(self.id, ''.join(seq)) line = f.readline() if not line.startswith('BaseQuality : '): raise Error("Error reading caf file. Expected line starting with 'BaseQuality : ...'") quals = [int(x) for x in f.readline().rstrip().split()] self.seq = self.seq.to_Fastq(quals) line = f.readline() assert line == '\n' line = f.readline() while line not in ['', '\n']: a = line.rstrip().split() if a[0] == 'Insert_size': self.insert_min, self.insert_max = int(a[1]), int(a[2]) elif a[0] == 'Ligation_no': self.ligation = a[1] elif a[0] == 'Clone': self.clone = a[1] elif a[0] == 'Clipping' and a[1] == 'QUAL': self.clip_start, self.clip_end = int(a[2]) - 1, int(a[3]) - 1 line = f.readline() return True Fastaq-3.14.0/pyfastaq/genetic_codes.py000066400000000000000000000047621276201573500200340ustar00rootroot00000000000000# see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi codes = {} starts = {} #standard genetic code codes[1] = { 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': '*', 'TAG': '*', 'TGT': 'C', 'TGC': 'C', 'TGA': '*', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', } starts[1] = set([ 'TTG', 'CTG', 'ATG', ]) #mycoplasma genetic code codes[4] = { 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': '*', 'TAG': '*', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G' } starts[4] = set([ 'TTA', 'TTG', 'CTG', 'ATT', 'ATC', 'ATA', 'ATG', 'GTG', ]) # Bacterial, Archaeal and Plant Plastid Code codes[11] = codes[1] starts[11] = set([ 'TTG', 'CTG', 'ATT', 'ATC', 'ATA', 'ATG', 'GTG', ]) Fastaq-3.14.0/pyfastaq/intervals.py000066400000000000000000000073161276201573500172460ustar00rootroot00000000000000class Error (Exception): pass class Interval: '''A class to deal with intervals in a genome. Can do things like intersections, unions etc''' def __init__(self, start, end): try: self.start = int(start) self.end = int(end) except ValueError: raise Error('Error making interval from :"' + str(start) + '" and "' + str(end) + '"') if self.end < self.start: raise Error('Error making interval ' + str(self) + '. end < start.') def __len__(self): return self.end - self.start + 1 def __eq__(self, other): return type(other) is type(self) and self.__dict__ == other.__dict__ def __ne__(self, other): return not self.__eq__(other) def __str__(self): return '(' + str(self.start) + ',' + str(self.end) + ')' def __lt__(self, i): return self.start < i.start or (self.start == i.start and self.end < i.end) def __le__(self, i): return self.start < i.start or (self.start == i.start and self.end <= i.end) def distance_to_point(self, p): '''Returns the distance from the point to the interval. Zero if the point lies inside the interval.''' if self.start <= p <= self.end: return 0 else: return min(abs(self.start - p), abs(self.end - p)) def intersects(self, i): '''Returns true iff this interval intersects the interval i''' return self.start <= i.end and i.start <= self.end def contains(self, i): '''Returns true iff this interval contains the interval i''' return self.start <= i.start and i.end <= self.end def union(self, i): '''If intervals intersect, returns their union, otherwise returns None''' if self.intersects(i) or self.end + 1 == i.start or i.end + 1 == self.start: return Interval(min(self.start, i.start), max(self.end, i.end)) else: return None def union_fill_gap(self, i): '''Like union, but ignores whether the two intervals intersect or not''' return Interval(min(self.start, i.start), max(self.end, i.end)) def intersection(self, i): '''If intervals intersect, returns their intersection, otherwise returns None''' if self.intersects(i): return Interval(max(self.start, i.start), min(self.end, i.end)) else: return None def intersection(l1, l2): '''Returns intersection of two lists. Assumes the lists are sorted by start positions''' if len(l1) == 0 or len(l2) == 0: return [] out = [] l2_pos = 0 for l in l1: while l2_pos < len(l2) and l2[l2_pos].end < l.start: l2_pos += 1 if l2_pos == len(l2): break while l2_pos < len(l2) and l.intersects(l2[l2_pos]): out.append(l.intersection(l2[l2_pos])) l2_pos += 1 l2_pos = max(0, l2_pos - 1) return out def merge_overlapping_in_list(l): '''Sorts list, merges any overlapping intervals, and also adjacent intervals. e.g. [0,1], [1,2] would be merge to [0,.2].''' i = 0 l.sort() while i < len(l) - 1: u = l[i].union(l[i+1]) if u is not None: l[i] = u l.pop(i+1) else: i += 1 def remove_contained_in_list(l): '''Sorts list in place, then removes any intervals that are completely contained inside another interval''' i = 0 l.sort() while i < len(l) - 1: if l[i+1].contains(l[i]): l.pop(i) elif l[i].contains(l[i+1]): l.pop(i+1) else: i += 1 def length_sum_from_list(l): '''Returns total length of intervals from a list''' return sum([len(x) for x in l]) Fastaq-3.14.0/pyfastaq/runners/000077500000000000000000000000001276201573500163525ustar00rootroot00000000000000Fastaq-3.14.0/pyfastaq/runners/__init__.py000066400000000000000000000000001276201573500204510ustar00rootroot00000000000000Fastaq-3.14.0/pyfastaq/runners/acgtn_only.py000066400000000000000000000007171276201573500210660ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Replaces any character that is not one of acgtACGTnN with an N', usage = 'fastaq acgtn_only [options] ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.acgtn_only(options.infile, options.outfile) Fastaq-3.14.0/pyfastaq/runners/add_indels.py000066400000000000000000000101671276201573500210170ustar00rootroot00000000000000import argparse import sys import random from pyfastaq import sequences, utils, intervals def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq add_indels [options] ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') parser.add_argument('-d','--delete', action='append', help='Delete the given bases from the given sequence. Format same as samtools view: name:start-end. This option can be used multiple times (once for each region to delete). Overlapping coords will be merged before deleting', metavar='Name:start:bases') parser.add_argument('--delete_range', help='Deletes bases starting at position P in each sequence of the input file. Deletes start + (n-1)*step bases from sequence n.', metavar='P,start,step') parser.add_argument('-i','--insert', action='append', help='Insert a random string of bases at the given position. Format is name:position:number_to_add. Bases are added after the position. This option can be used multiple times', metavar='Name:start:bases') parser.add_argument('--insert_range', help='Inserts random bases starting after position P in each sequence of the input file. Inserts start + (n-1)*step bases into sequence n.', metavar='P,start,step') options = parser.parse_args() test_ops = [int(x is not None) for x in [options.delete, options.insert, options.delete_range, options.insert_range]] if sum(test_ops) != 1: print('Must use one of --delete, --insert, --delete_range, --insert_range. Cannot continue', file=sys.stderr) sys.exit(1) def range2dic(range_in): if range_in is None: return {} (pos, start, step) = range_in.split(',') d = {} d['pos'] = int(pos) - 1 d['bases'] = int(start) d['step'] = int(step) return d delete_range = range2dic(options.delete_range) insert_range = range2dic(options.insert_range) # convert the -d regions into sequence name, start and end coords to_delete = {} if options.delete: for s in options.delete: id, coords = s.rsplit(':') start, end = [int(x)-1 for x in coords.split('-')] if id not in to_delete: to_delete[id] = [] to_delete[id].append(intervals.Interval(start, end)) to_insert = {} if options.insert: for s in options.insert: id, pos, bases = s.rsplit(':',2) pos = int(pos) - 1 bases = int(bases) if id not in to_insert: to_insert[id] = [] to_insert[id].append((pos, bases)) assert len(to_delete) * len(to_insert) == 0 # merge overlapping regions to be deleted for l in to_delete.values(): intervals.merge_overlapping_in_list(l) # sort positions to be inserted for l in to_insert.values(): l.sort() # read in the fasta/q file and print outfile with deleted sequences seq_reader = sequences.file_reader(options.infile) f = utils.open_file_write(options.outfile) for seq in seq_reader: if seq.id in to_delete: # delete regions for this sequence, but start at the end so the # coords don't get messed up after the first deletion for inter in reversed(to_delete[seq.id]): seq.seq = seq.seq[:inter.start] + seq.seq[inter.end + 1:] elif options.delete_range: seq.seq = seq.seq[:delete_range['pos']] + seq.seq[delete_range['pos'] + delete_range['bases']:] delete_range['bases'] += delete_range['step'] elif seq.id in to_insert: for pos, bases in reversed(to_insert[seq.id]): seq.seq = seq.seq[:pos + 1] + ''.join([random.choice('ACGT') for x in range(bases)]) + seq.seq[pos + 1:] elif options.insert_range: seq.seq = seq.seq[:insert_range['pos'] + 1] + ''.join([random.choice('ACGT') for x in range(insert_range['bases'])]) + seq.seq[insert_range['pos'] + 1:] insert_range['bases'] += insert_range['step'] print(seq, file=f) utils.close(f) Fastaq-3.14.0/pyfastaq/runners/caf_to_fastq.py000066400000000000000000000015761276201573500213660ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Converts CAF file to FASTQ format', usage = 'fastaq caf_to_fastq [options] ') parser.add_argument('infile', help='Name of input CAF file.') parser.add_argument('outfile', help='Name of output FASTQ file') parser.add_argument('-c', '--clip', action='store_true', help='Use clipping info to clip reads, if present in the input CAF file (as lines of the form "Clipping QUAL start end"). Default is to not clip') parser.add_argument('-l', '--min_length', type=int, help='Minimum length of sequence to output [%(default)s]', default=1, metavar='INT') options = parser.parse_args() tasks.caf_to_fastq( options.infile, options.outfile, trim=options.clip, min_length=options.min_length ) Fastaq-3.14.0/pyfastaq/runners/capillary_to_pairs.py000066400000000000000000000013121276201573500226010ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Given a file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with /1 and /2', usage = 'fastaq capillary_to_pairs ') parser.add_argument('infile', help='Name of input fasta/q file') parser.add_argument('outprefix', help='Prefix of output files', metavar='outfiles prefix') options = parser.parse_args() tasks.capillary_to_pairs(options.infile, options.outprefix) Fastaq-3.14.0/pyfastaq/runners/chunker.py000066400000000000000000000030101276201573500203550ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Splits a multi sequence file into separate files. Splits sequences into chunks of a fixed size. Aims for chunk_size chunks in each file, but allows a little extra, so chunk can be up to (chunk_size + tolerance), to prevent tiny chunks made from the ends of sequences', usage = 'fastaq chunker [options] ') parser.add_argument('infile', help='Name of input file to be split') parser.add_argument('out', help='Prefix of output file. If --onefile used, then name of single output file') parser.add_argument('chunk_size', type=int, help='Size of each chunk') parser.add_argument('tolerance', type=int, help='Tolerance allowed in chunk size') parser.add_argument('--onefile', action='store_true', help='Output all the sequences in one file') parser.add_argument('--skip_all_Ns', action='store_true', help='Do not output any sequence that consists of all Ns') options = parser.parse_args() if options.onefile: tasks.split_by_fixed_size_onefile( options.infile, options.out, options.chunk_size, options.tolerance, skip_if_all_Ns=options.skip_all_Ns ) else: tasks.split_by_fixed_size( options.infile, options.out, options.chunk_size, options.tolerance, skip_if_all_Ns=options.skip_all_Ns ) Fastaq-3.14.0/pyfastaq/runners/count_sequences.py000066400000000000000000000005731276201573500221340ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Prints the number of sequences in input file to stdout', usage = 'fastaq count_sequences ') parser.add_argument('infile', help='Name of input file') options = parser.parse_args() print(tasks.count_sequences(options.infile)) Fastaq-3.14.0/pyfastaq/runners/deinterleave.py000066400000000000000000000014771276201573500214040ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Deinterleaves sequence file, so that reads are written alternately between two output files', usage = 'fastaq deinterleave [options] ') parser.add_argument('--fasta_out', action='store_true', help='Use this to write output as fasta (default is same as input)', default=False) parser.add_argument('infile', help='Name of fasta/q file to be deinterleaved') parser.add_argument('out_fwd', help='Name of output fasta/q file of forwards reads') parser.add_argument('out_rev', help='Name of output fasta/q file of reverse reads') options = parser.parse_args() tasks.deinterleave(options.infile, options.out_fwd, options.out_rev, fasta_out=options.fasta_out) Fastaq-3.14.0/pyfastaq/runners/enumerate_names.py000066400000000000000000000021011276201573500220660ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Renames sequences in a file, calling them 1,2,3... etc', usage = 'fastaq enumerate_names [options] ') parser.add_argument('--start_index', type=int, help='Starting number [%(default)s]', default=1) parser.add_argument('--rename_file', help='If used, will write a file of old name to new name') parser.add_argument('--keep_suffix', action='store_true', help='Use this to keep a /1 or /2 suffix at the end of each name') parser.add_argument('--suffix', help='Add the given string to the end of every name', default=None) parser.add_argument('infile', help='Name of fasta/q file to be read') parser.add_argument('outfile', help='Name of output fasta/q file') options = parser.parse_args() tasks.enumerate_names(options.infile, options.outfile, start_index=options.start_index, keep_illumina_suffix=options.keep_suffix, rename_file=options.rename_file, suffix=options.suffix) Fastaq-3.14.0/pyfastaq/runners/expand_nucleotides.py000066400000000000000000000011411276201573500225760ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Makes all combinations of sequences in input file by using all possibilities of redundant bases. e.g. ART could be AAT or AGT. Assumes input is nucleotides, not amino acids', usage = 'fastaq expand_nucleotides ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.expand_nucleotides( options.infile, options.outfile, ) Fastaq-3.14.0/pyfastaq/runners/fasta_to_fastq.py000066400000000000000000000011131276201573500217160ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq fasta_to_fastq ') parser.add_argument('fasta', help='Name of input FASTA file', metavar='fasta in') parser.add_argument('qual', help='Name of input quality scores file', metavar='qual in') parser.add_argument('outfile', help='Name of output FASTQ file', metavar='fastq out') options = parser.parse_args() tasks.fasta_to_fastq(options.fasta, options.qual, options.outfile) Fastaq-3.14.0/pyfastaq/runners/filter.py000066400000000000000000000040421276201573500202110ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Filters a sequence file by sequence length and/or by name matching a regular expression', usage = 'fastaq filter [options] ') parser.add_argument('--min_length', type=int, help='Minimum length of sequence to keep [%(default)s]', default=0, metavar='INT') parser.add_argument('--max_length', type=float, help='Maximum length of sequence to keep [%(default)s]', default=float('inf'), metavar='INT') parser.add_argument('--regex', help='If given, only reads with a name matching the regular expression will be kept') parser.add_argument('--ids_file', help='If given, only reads whose ID is in th given file will be used. One ID per line of file.', metavar='FILENAME') parser.add_argument('-v', '--invert', action='store_true', help='Only keep sequences that do not match the filters') mate_group = parser.add_argument_group('Mate file for read pairs options') mate_group.add_argument('--mate_in', help='Name of mates input file. If used, must also provide --mate_out', metavar='FILENAME') mate_group.add_argument('--mate_out', help='Name of mates output file', metavar='FILENAME') mate_group.add_argument('--both_mates_pass', action='store_true', help='By default, if either mate passes filter, then both reads output. Use this flag to require that both reads of a pair pass the filter') parser.add_argument('infile', help='Name of input file to be filtered') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.filter(options.infile, options.outfile, minlength=options.min_length, maxlength=options.max_length, regex=options.regex, ids_file=options.ids_file, invert=options.invert, mate_in=options.mate_in, mate_out=options.mate_out, both_mates_pass=options.both_mates_pass, ) Fastaq-3.14.0/pyfastaq/runners/get_ids.py000066400000000000000000000006611276201573500203450ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Gets IDs from each sequence in input file', usage = 'fastaq get_ids ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.get_ids(options.infile, options.outfile) Fastaq-3.14.0/pyfastaq/runners/get_seq_flanking_gaps.py000066400000000000000000000013351276201573500232400ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq get_seq_flanking_gaps [options] ') parser.add_argument('--left', type=int, help='Number of bases to get to left of gap [%(default)s]', default=25, metavar='INT') parser.add_argument('--right', type=int, help='Number of bases to get to right of gap [%(default)s]', default=25, metavar='INT') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.get_seqs_flanking_gaps(options.infile, options.outfile, options.left, options.right) Fastaq-3.14.0/pyfastaq/runners/interleave.py000066400000000000000000000015471276201573500210710ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq interleave ') parser.add_argument('--suffix1', help='Suffix to add to all names from infile_1 (if suffix not already present)') parser.add_argument('--suffix2', help='Suffix to add to all names from infile_2 (if suffix not already present)') parser.add_argument('infile_1', help='Name of first input file') parser.add_argument('infile_2', help='Name of second input file') parser.add_argument('outfile', help='Name of output file of interleaved reads') options = parser.parse_args() tasks.interleave( options.infile_1, options.infile_2, options.outfile, suffix1=options.suffix1, suffix2=options.suffix2 ) Fastaq-3.14.0/pyfastaq/runners/make_random_contigs.py000066400000000000000000000025271276201573500227350ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Makes a multi-FASTA file of random sequences, all of the same length. Each base has equal chance of being A,C,G or T', usage = 'fastaq make_random_contigs [options] ') parser.add_argument('--first_number', type=int, help='If numbering the sequences, the first sequence gets this number [%(default)s]', default=1) parser.add_argument('--name_by_letters', action='store_true', help='Name the contigs A,B,C,... will start at A again if you get to Z') parser.add_argument('--prefix', help='Prefix to add to start of every sequence name', default='') parser.add_argument('--seed', type=int, help='Seed for random number generator. Default is to use python\'s default', default=None) parser.add_argument('contigs', type=int, help='Nunber of contigs to make') parser.add_argument('length', type=int, help='Length of each contig') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.make_random_contigs( options.contigs, options.length, options.outfile, name_by_letters=options.name_by_letters, prefix=options.prefix, seed=options.seed, first_number=options.first_number ) Fastaq-3.14.0/pyfastaq/runners/merge.py000066400000000000000000000011051276201573500200200ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq merge [options] ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') parser.add_argument('-n', '--name', help='Name of sequence in output file [%(default)s]', default='union') options = parser.parse_args() tasks.merge_to_one_seq( options.infile, options.outfile, seqname=options.name ) Fastaq-3.14.0/pyfastaq/runners/replace_bases.py000066400000000000000000000010761276201573500215200ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq replace_bases ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') parser.add_argument('old', help='Base to be replaced') parser.add_argument('new', help='Replace with this letter') options = parser.parse_args() tasks.replace_bases(options.infile, options.outfile, options.old, options.new) Fastaq-3.14.0/pyfastaq/runners/reverse_complement.py000066400000000000000000000006471276201573500226310ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq reverse_complement ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.reverse_complement(options.infile, options.outfile) Fastaq-3.14.0/pyfastaq/runners/scaffolds_to_contigs.py000066400000000000000000000013001276201573500231120ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input', usage = 'fastaq scaffolds_to_contigs [options] ') parser.add_argument('--number_contigs', action='store_true', help='Use this to enumerate contig names 1,2,3,... within each scaffold') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output contigs file') options = parser.parse_args() tasks.scaffolds_to_contigs(options.infile, options.outfile, number_contigs=options.number_contigs) Fastaq-3.14.0/pyfastaq/runners/search_for_seq.py000066400000000000000000000013651276201573500217140ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Searches for an exact match on a given string and its reverse complement, in every sequence of input sequence file. Case insensitive. Guaranteed to find all hits', usage = 'fastaq search_for_seq [options] ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of outputfile. Tab-delimited output: sequence name, position, strand') parser.add_argument('search_string', help='String to search for in the sequences') options = parser.parse_args() tasks.search_for_seq(options.infile, options.outfile, options.search_string) Fastaq-3.14.0/pyfastaq/runners/sequence_trim.py000066400000000000000000000027271276201573500215770ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Trims sequences off the start of all sequences in a pair of sequence files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming', usage = 'fastaq sequence_trim [options] ') parser.add_argument('--min_length', type=int, help='Minimum length of output sequences [%(default)s]', default=50, metavar='INT') parser.add_argument('--revcomp', action='store_true', help='Trim the end of each sequence if it matches the reverse complement. This option is intended for PCR primer trimming') parser.add_argument('infile_1', help='Name of forward fasta/q file to be trimmed') parser.add_argument('infile_2', help='Name of reverse fasta/q file to be trimmed') parser.add_argument('outfile_1', help='Name of output forward fasta/q file') parser.add_argument('outfile_2', help='Name of output reverse fasta/q file') parser.add_argument('trim_seqs', help='Name of file of sequences to search for at the start of each input sequence') options = parser.parse_args() tasks.sequence_trim( options.infile_1, options.infile_2, options.outfile_1, options.outfile_2, options.trim_seqs, min_length=options.min_length, check_revcomp=options.revcomp ) Fastaq-3.14.0/pyfastaq/runners/sort_by_size.py000066400000000000000000000011521276201573500214360ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq sort_by_size [options] ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') parser.add_argument('-r', '--reverse', action='store_true', help='Sort by shortest first instead of the default of longest first') options = parser.parse_args() tasks.sort_by_size( options.infile, options.outfile, smallest_first=options.reverse ) Fastaq-3.14.0/pyfastaq/runners/split_by_base_count.py000066400000000000000000000016531276201573500227600ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Splits a multi sequence file into separate files. Does not split sequences. Puts up to max_bases into each split file. The exception is that any sequence longer than max_bases is put into its own file.', usage = 'fastaq split_by_base_count [options] ') parser.add_argument('infile', help='Name of input file to be split') parser.add_argument('outprefix', help='Name of output file') parser.add_argument('max_bases', type=int, help='Max bases in each output split file', metavar='max_bases') parser.add_argument('--max_seqs', type=int, help='Max number of sequences in each output split file [no limit]', metavar='INT') options = parser.parse_args() tasks.split_by_base_count(options.infile, options.outprefix, options.max_bases, options.max_seqs) Fastaq-3.14.0/pyfastaq/runners/strip_illumina_suffix.py000066400000000000000000000006551276201573500233510ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq strip_illumina_suffix ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.strip_illumina_suffix(options.infile, options.outfile) Fastaq-3.14.0/pyfastaq/runners/to_boulderio.py000066400000000000000000000007431276201573500214160ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Converts input sequence file into "Boulder-IO" format, which is used by primer3', usage = 'fastaq to_boulderio ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output files') options = parser.parse_args() tasks.to_boulderio(options.infile, options.outfile) Fastaq-3.14.0/pyfastaq/runners/to_fake_qual.py000066400000000000000000000011241276201573500213540ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq to_fake_qual [options] ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') parser.add_argument('-q', '--qual', type=int, help='Quality score to assign to all bases [%(default)s]', default=40) options = parser.parse_args() tasks.fastaq_to_fake_qual( options.infile, options.outfile, q=options.qual ) Fastaq-3.14.0/pyfastaq/runners/to_fasta.py000066400000000000000000000021321276201573500205220ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq to_fasta [options] ') parser.add_argument('infile', help='Name of input file. Can be any of FASTA, FASTQ, GFF3, EMBL, GBK, Phylip') parser.add_argument('outfile', help='Name of output file') parser.add_argument('-l', '--line_length', type=int, help='Number of bases on each sequence line of output file. Set to zero for no linebreaks in sequences [%(default)s]', default=60) parser.add_argument('-s', '--strip_after_whitespace', action='store_true', help='Remove everything after first whitespace in every sequence name') parser.add_argument('-u', '--check_unique', action='store_true', help='Die if any of the output sequence names are not unique') options = parser.parse_args() tasks.to_fasta( options.infile, options.outfile, line_length=options.line_length, strip_after_first_whitespace=options.strip_after_whitespace, check_unique=options.check_unique ) Fastaq-3.14.0/pyfastaq/runners/to_mira_xml.py000066400000000000000000000006541276201573500212430ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq to_mira_xml ') parser.add_argument('infile', help='Name of input fasta/q file') parser.add_argument('xml_out', help='Name of output xml file') options = parser.parse_args() tasks.fastaq_to_mira_xml(options.infile, options.xml_out) Fastaq-3.14.0/pyfastaq/runners/to_orfs_gff.py000066400000000000000000000012131276201573500212160ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Writes a GFF file of open reading frames from a sequence file', usage = 'fastaq to_orfs_gff [options] ') parser.add_argument('--min_length', type=int, help='Minimum length of ORF, in nucleotides [%(default)s]', default=300, metavar='INT') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output GFF file') options = parser.parse_args() tasks.fastaq_to_orfs_gff(options.infile, options.outfile, min_length=options.min_length) Fastaq-3.14.0/pyfastaq/runners/to_perfect_reads.py000066400000000000000000000102151276201573500222330ustar00rootroot00000000000000import argparse import random from math import floor, ceil import sys from pyfastaq import sequences, utils def run(description): parser = argparse.ArgumentParser( description = 'Makes perfect paired end fastq reads from a sequence file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved FASTQ file.', usage = 'fastaq to_perfect_reads [options] ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') parser.add_argument('mean_insert', type=int, help='Mean insert size of read pairs', metavar='mean insert size') parser.add_argument('insert_std', type=float, help='Standard devation of insert size', metavar='insert std deviation') parser.add_argument('coverage', type=float, help='Mean coverage of the reads', metavar='mean coverage') parser.add_argument('readlength', type=int, help='Length of each read', metavar='read length') parser.add_argument('--fragments', help='Write FASTA sequences of fragments (i.e. read pairs plus sequences in between them) to the given filename', metavar='FILENAME') parser.add_argument('--no_n', action='store_true', help='Don\'t allow any N or n characters in the reads') parser.add_argument('--seed', type=int, help='Seed for random number generator. Default is to use python\'s default', default=None, metavar='INT') options = parser.parse_args() random.seed(a=options.seed) seq_reader = sequences.file_reader(options.infile) fout = utils.open_file_write(options.outfile) pair_counter = 1 if options.fragments: fout_frags = utils.open_file_write(options.fragments) for ref in seq_reader: # check if current seq is long enough if len(ref) < options.mean_insert + 4 * options.insert_std: print('Warning, sequence ', ref.id, ' too short. Skipping it...', file=sys.stderr) continue # work out how many reads to simulate read_pairs = int(0.5 * options.coverage * len(ref) / options.readlength) # it's possible that we pick the same fragment twice, in which case the # reads would get the same name. So remember the frag coords used_fragments = {} # (middle_position, length) => count # do the simulation: pick insert size from normal distribution, and # position in genome from uniform distribution x = 0 while x < read_pairs: isize = int(random.normalvariate(options.mean_insert, options.insert_std)) while isize > len(ref) or isize < options.readlength: isize = int(random.normalvariate(options.mean_insert, options.insert_std)) middle_pos = random.randint(ceil(0.5 *isize), floor(len(ref) - 0.5 * isize)) read_start1 = int(middle_pos - ceil(0.5 * isize)) read_start2 = read_start1 + isize - options.readlength readname = ':'.join([ref.id, str(pair_counter), str(read_start1+1), str(read_start2+1)]) fragment = (middle_pos, isize) if fragment in used_fragments: used_fragments[fragment] += 1 readname += '.dup.' + str(used_fragments[fragment]) else: used_fragments[fragment] = 1 read1 = sequences.Fastq(readname + '/1', ref.seq[read_start1:read_start1 + options.readlength], 'I' * options.readlength) read2 = sequences.Fastq(readname + '/2', ref.seq[read_start2:read_start2 + options.readlength], 'I' * options.readlength) if options.no_n and ('n' in read1.seq or 'N' in read1.seq or 'n' in read2.seq or 'N' in read2.seq): continue read2.revcomp() print(read1, file=fout) print(read2, file=fout) if options.fragments: frag = sequences.Fasta(readname, ref.seq[read_start1:read_start2 + options.readlength]) print(frag, file=fout_frags) pair_counter += 1 x += 1 utils.close(fout) if options.fragments: utils.close(fout_frags) Fastaq-3.14.0/pyfastaq/runners/to_random_subset.py000066400000000000000000000031061276201573500222730ustar00rootroot00000000000000import argparse import sys import random from pyfastaq import sequences, utils def run(description): parser = argparse.ArgumentParser( description = 'Takes a random subset of reads from a sequence file and optionally the corresponding read ' + 'from a mates file. Output is interleaved if mates file given', usage = 'fastaq to_random_subset [options] ') parser.add_argument('--mate_file', help='Name of mates file') parser.add_argument('--seed', help='Seed for random number generator. If not given, python\'s default is used', metavar='INT') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') parser.add_argument('percent', type=float, help='Per cent probability of keeping any given read (pair) in [0,100]', metavar='FLOAT') options = parser.parse_args() random.seed(a=options.seed) seq_reader = sequences.file_reader(options.infile) fout = utils.open_file_write(options.outfile) if options.mate_file: mate_seq_reader = sequences.file_reader(options.mate_file) for seq in seq_reader: if options.mate_file: try: mate_seq = next(mate_seq_reader) except StopIteration: print('Error! Didn\'t get mate for read', seq.id, file=sys.stderr) sys.exit(1) if 100 * random.random() <= options.percent: print(seq, file=fout) if options.mate_file: print(mate_seq, file=fout) utils.close(fout) Fastaq-3.14.0/pyfastaq/runners/to_tiling_bam.py000066400000000000000000000062071276201573500215400ustar00rootroot00000000000000import argparse import sys import os from pyfastaq import sequences, utils def run(description): parser = argparse.ArgumentParser( description = 'Takes a sequence file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome', usage = 'fastaq to_tiling_bam [options] ', epilog = 'Important: assumes that samtools is in your path') parser.add_argument('infile', help='Name of input fasta/q file') parser.add_argument('read_length', type=int, help='Length of reads') parser.add_argument('read_step', type=int, help='Distance between start of each read') parser.add_argument('read_prefix', help='Prefix of read names') parser.add_argument('outfile', help='Name of output BAM file') parser.add_argument('--qual_char', help='Character to use for quality score [%(default)s]', default='I') parser.add_argument('--read_group', help='Add the given read group ID to all reads [%(default)s]' ,default='42') options = parser.parse_args() # make a header first - we need to add the @RG line to the default header made by samtools tmp_empty_file = options.outfile + '.tmp.empty' f = utils.open_file_write(tmp_empty_file) utils.close(f) try: f = os.popen('samtools view -H -T ' + options.infile + ' ' + tmp_empty_file) except IOError: print('Error making tmp header file', file=sys.stderr) sys.exit(1) header_lines = f.readlines() header_lines.append('@RG\tID:' + options.read_group + '\tSM:FAKE') f.close() os.unlink(tmp_empty_file) seq_reader = sequences.file_reader(options.infile) try: f = os.popen('samtools view -hbS - > ' + options.outfile, 'w') except IOError: print("Error opening for writing BAM file '" + options.outfile + "'", file=sys.stderr) sys.exit(1) print(''.join(header_lines), file=f) for seq in seq_reader: end_range = len(seq) if len(seq) < options.read_length: end_range = 1 for i in range(0, end_range, options.read_step): if len(seq) <= options.read_length: start = 0 end = len(seq) - 1 else: start = i end = start + options.read_length - 1 if end > len(seq) - 1: end = len(seq) - 1 start = end - options.read_length + 1 read = sequences.Fastq(options.read_prefix + ':' + seq.id + ':' + str(start + 1) + ':' + str(end + 1), seq[start:end+1], options.qual_char * (end - start + 1)) print ('\t'.join([read.id, '0', seq.id, str(start + 1), '60', str(len(read)) + 'M', '*', '*', '*', read.seq, read.qual, 'RG:Z:' + options.read_group]), file=f) if end == len(seq) - 1: break f.close() Fastaq-3.14.0/pyfastaq/runners/to_unique_by_id.py000066400000000000000000000011211276201573500220750ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Removes duplicate sequences from input file, based on their names. If the same name is found more than once, then the longest sequence is kept. Order of sequences is preserved in output', usage = 'fastaq to_unique_by_id ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.to_unique_by_id(options.infile, options.outfile) Fastaq-3.14.0/pyfastaq/runners/translate.py000066400000000000000000000011631276201573500207220ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Translates all sequences in input file. Output is always FASTA format', usage = 'fastaq translate [options] ') parser.add_argument('--frame', type=int, choices=[0,1,2], help='Frame to translate [%(default)s]', default=0) parser.add_argument('infile', help='Name of file to be translated') parser.add_argument('outfile', help='Name of output FASTA file') options = parser.parse_args() tasks.translate(options.infile, options.outfile, frame=options.frame) Fastaq-3.14.0/pyfastaq/runners/trim_Ns_at_end.py000066400000000000000000000007731276201573500216600ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Trims any Ns off each sequence in input file. Does nothing to gaps in the middle, just trims the ends', usage = 'fastaq trim_Ns_at_end ') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.trim_Ns_at_end(options.infile, options.outfile) Fastaq-3.14.0/pyfastaq/runners/trim_contigs.py000066400000000000000000000013761276201573500214340ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = 'Trims a set number of bases off the end of every contig, so gaps get bigger and contig ends are removed. Bases are replaced with Ns. Any sequence that ends up as all Ns is lost', usage = 'fastaq trim_contigs [options] ') parser.add_argument('--trim_number', type=int, help='Number of bases to trim around each gap, and off ends of each sequence [%(default)s]', default=100) parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.trim_contigs(options.infile, options.outfile, options.trim_number) Fastaq-3.14.0/pyfastaq/runners/trim_ends.py000066400000000000000000000012101276201573500207020ustar00rootroot00000000000000import argparse from pyfastaq import tasks def run(description): parser = argparse.ArgumentParser( description = description, usage = 'fastaq trim_ends ') parser.add_argument('infile', help='Name of input file') parser.add_argument('start_trim', type=int, help='Number of bases to trim off start') parser.add_argument('end_trim', type=int, help='Number of bases to trim off end') parser.add_argument('outfile', help='Name of output file') options = parser.parse_args() tasks.trim(options.infile, options.outfile, options.start_trim, options.end_trim) Fastaq-3.14.0/pyfastaq/runners/version.py000066400000000000000000000001071276201573500204070ustar00rootroot00000000000000import pyfastaq def run(description): print(pyfastaq.__version__) Fastaq-3.14.0/pyfastaq/sequences.py000066400000000000000000000561551276201573500172370ustar00rootroot00000000000000import copy import re import string import random import itertools from pyfastaq import utils, intervals, genetic_codes class Error (Exception): pass # python 3's seek is glacially slow. When we read a fasta file, we know # we've reached the end of a sequence when we get a new line starting with # '>'. Instead of using seek and tell, we just remember the previous line # of the file, for any given filehandle previous_lines = {} genetic_code = 1 redundant_nts = { 'R': ('A', 'G'), 'Y': ('C', 'T'), 'S': ('C', 'G'), 'W': ('A', 'T'), 'K': ('G', 'T'), 'M': ('A', 'C'), 'B': ('C', 'G', 'T'), 'D': ('A', 'G', 'T'), 'H': ('A', 'C', 'T'), 'V': ('A', 'C', 'G'), 'N': ('A', 'C', 'G', 'T') } def file_reader(fname, read_quals=False): '''Iterates over a FASTA or FASTQ file, yielding the next sequence in the file until there are no more sequences''' f = utils.open_file_read(fname) line = f.readline() phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') gbk_regex = re.compile('^LOCUS\s+\S') if line.startswith('>'): seq = Fasta() previous_lines[f] = line elif line.startswith('##gff-version 3'): seq = Fasta() # if a GFF file, need to skip past all the annotation # and get to the fasta sequences at the end of the file while not line.startswith('>'): line = f.readline() if not line: utils.close(f) raise Error('No sequences found in GFF file "' + fname + '"') seq = Fasta() previous_lines[f] = line elif line.startswith('ID ') and line[5] != ' ': seq = Embl() previous_lines[f] = line elif gbk_regex.search(line): seq = Embl() previous_lines[f] = line elif line.startswith('@'): seq = Fastq() previous_lines[f] = line elif phylip_regex.search(line): # phylip format could be interleaved or not, need to look at next # couple of lines to figure that out. Don't expect these files to # be too huge, so just store all the sequences in memory number_of_seqs, bases_per_seq = line.strip().split() number_of_seqs = int(number_of_seqs) bases_per_seq = int(bases_per_seq) got_blank_line = False first_line = line seq_lines = [] while 1: line = f.readline() if line == '': break elif line == '\n': got_blank_line = True else: seq_lines.append(line.rstrip()) utils.close(f) if len(seq_lines) == 1 or len(seq_lines) == number_of_seqs: sequential = True elif seq_lines[0][10] != ' ' and seq_lines[1][10] == ' ': sequential = True else: sequential = False # if the 11th char of second sequence line is a space, then the file is sequential, e.g.: # GAGCCCGGGC AATACAGGGT AT # as opposed to: # Salmo gairAAGCCTTGGC AGTGCAGGGT if sequential: current_id = None current_seq = '' for line in seq_lines: if len(current_seq) == bases_per_seq or len(current_seq) == 0: if current_id is not None: yield Fasta(current_id, current_seq.replace('-', '')) current_seq = '' current_id, new_bases = line[0:10].rstrip(), line.rstrip()[10:] else: new_bases = line.rstrip() current_seq += new_bases.replace(' ','') yield Fasta(current_id, current_seq.replace('-', '')) else: # seaview files start all seqs at pos >=12. Other files start # their sequence at the start of the line if seq_lines[number_of_seqs + 1][0] == ' ': first_gap_pos = seq_lines[0].find(' ') end_of_gap = first_gap_pos while seq_lines[0][end_of_gap] == ' ': end_of_gap += 1 first_seq_base = end_of_gap else: first_seq_base = 10 seqs = [] for i in range(number_of_seqs): name, bases = seq_lines[i][0:first_seq_base].rstrip(), seq_lines[i][first_seq_base:] seqs.append(Fasta(name, bases)) for i in range(number_of_seqs, len(seq_lines)): seqs[i%number_of_seqs].seq += seq_lines[i] for fa in seqs: fa.seq = fa.seq.replace(' ','').replace('-','') yield fa return elif line == '': utils.close(f) return else: utils.close(f) raise Error('Error determining file type from file "' + fname + '". First line is:\n' + line.rstrip()) try: while seq.get_next_from_file(f, read_quals): yield seq finally: utils.close(f) class Fasta: '''Class to store and manipulate FASTA sequences. They have two things: a name and a sequence''' # this defines the line length when printing sequences line_length = 60 def _get_id_from_header_line(self, line): if line.startswith('>'): return line.rstrip()[1:] else: raise Error('Error! expected line starting with ">", but got this:\n', line) def __init__(self, id_in=None, seq_in=None): self.id = id_in self.seq = seq_in def __eq__(self, other): return type(other) is type(self) and self.__dict__ == other.__dict__ def __ne__(self, other): return not self.__eq__(other) def __len__(self): return len(self.seq) def subseq(self, start, end): '''Returns Fasta object with the same name, of the bases from start to end, but not including end''' return Fasta(self.id, self.seq[start:end]) def split_capillary_id(self): '''Gets the prefix and suffix of an name of a capillary read, e.g. xxxxx.p1k or xxxx.q1k. Returns a tuple (prefix, suffx)''' try: a = self.id.rsplit('.', 1) if a[1].startswith('p'): dir = 'fwd' elif a[1].startswith('q'): dir = 'rev' else: dir = 'unk' return {'prefix': a[0], 'dir': dir, 'suffix':a[1]} except: raise Error('Error in split_capillary_id() on ID', self.id) def expand_nucleotides(self): '''Assumes sequence is nucleotides. Returns list of all combinations of redundant nucleotides. e.g. R is A or G, so CRT would have combinations CAT and CGT''' s = list(self.seq) for i in range(len(s)): if s[i] in redundant_nts: s[i] = ''.join(redundant_nts[s[i]]) seqs = [] for x in itertools.product(*s): seqs.append(Fasta(self.id + '.' + str(len(seqs) + 1), ''.join(x))) return seqs def strip_after_first_whitespace(self): '''Removes everything in the name after the first whitespace character''' self.id = self.id.split()[0] def strip_illumina_suffix(self): '''Removes any trailing /1 or /2 off the end of the name''' if self.id.endswith('/1') or self.id.endswith('/2'): self.id = self.id[:-2] def revcomp(self): '''Reverse complements the sequence''' self.seq = self.seq.translate(str.maketrans("ATCGatcg", "TAGCtagc"))[::-1] def is_all_Ns(self, start=0, end=None): '''Returns true if the sequence is all Ns (upper or lower case)''' if end is not None: if start > end: raise Error('Error in is_all_Ns. Start coord must be <= end coord') end += 1 else: end = len(self) if len(self) == 0: return False else: return re.search('[^Nn]', self.seq[start:end]) is None def trim_Ns(self): '''Removes any leading or trailing N or n characters from the sequence''' self.seq = self.seq.strip('Nn') def add_insertions(self, skip=10, window=1, test=False): '''Adds a random base within window bases around every skip bases. e.g. skip=10, window=1 means a random base added somwhere in theintervals [9,11], [19,21] ... ''' assert 2 * window < skip new_seq = list(self.seq) for i in range(len(self) - skip, 0, -skip): pos = random.randrange(i - window, i + window + 1) base = random.choice(['A', 'C', 'G', 'T']) if test: base = 'N' new_seq.insert(pos, base) self.seq = ''.join(new_seq) def replace_bases(self, old, new): '''Replaces all occurrences of 'old' with 'new' ''' self.seq = self.seq.replace(old, new) def replace_non_acgt(self): '''Replace all non acgt characters with an N (case insensitive)''' self.seq = re.sub(r'''[^acgtACGTnN]''', 'N', self.seq) def replace_interval(self, start, end, new): '''Replaces the sequence from start to end with the sequence "new"''' if start > end or start > len(self) - 1 or end > len(self) - 1: raise Error('Error replacing bases ' + str(start) + '-' + str(end) + ' in sequence ' + self.id) self.seq = self.seq[0:start] + new + self.seq[end + 1:] def gaps(self, min_length = 1): '''Finds the positions of all gaps in the sequence that are at least min_length long. Returns a list of Intervals. Coords are zero-based''' gaps = [] regex = re.compile('N+', re.IGNORECASE) for m in regex.finditer(self.seq): if m.span()[1] - m.span()[0] + 1 >= min_length: gaps.append(intervals.Interval(m.span()[0], m.span()[1] - 1)) return gaps def contig_coords(self): '''Finds coords of contigs, i.e. everything that's not a gap (N or n). Returns a list of Intervals. Coords are zero-based''' # contigs are the opposite of gaps, so work out the coords from the gap coords gaps = self.gaps() if len(gaps) == 0: return [intervals.Interval(0, len(self) - 1)] coords = [0] for g in gaps: if g.start == 0: coords = [g.end + 1] else: coords += [g.start - 1, g.end + 1] if coords[-1] < len(self): coords.append(len(self) - 1) return [intervals.Interval(coords[i], coords[i+1]) for i in range(0, len(coords)-1,2)] def orfs(self, frame=0, revcomp=False): '''Returns a list of ORFs that the sequence has, starting on the given frame. Each returned ORF is an interval.Interval object. If revomp=True, then finds the ORFs of the reverse complement of the sequence.''' assert frame in [0,1,2] if revcomp: self.revcomp() aa_seq = self.translate(frame=frame).seq.rstrip('X') if revcomp: self.revcomp() orfs = _orfs_from_aa_seq(aa_seq) for i in range(len(orfs)): if revcomp: start = len(self) - (orfs[i].end * 3 + 3) - frame end = len(self) - (orfs[i].start * 3) - 1 - frame else: start = orfs[i].start * 3 + frame end = orfs[i].end * 3 + 2 + frame orfs[i] = intervals.Interval(start, end) return orfs def all_orfs(self, min_length=300): '''Finds all open reading frames in the sequence, that are at least as long as min_length. Includes ORFs on the reverse strand. Returns a list of ORFs, where each element is a tuple: (interval.Interval, bool) where bool=True means on the reverse strand''' orfs = [] for frame in [0,1,2]: for revcomp in [False, True]: orfs.extend([(t, revcomp) for t in self.orfs(frame=frame, revcomp=revcomp) if len(t)>=min_length]) return sorted(orfs, key=lambda t:t[0]) def is_complete_orf(self): '''Returns true iff length is >= 6, is a multiple of 3, and there is exactly one stop codon in the sequence and it is at the end''' if len(self) %3 != 0 or len(self) < 6: return False orfs = self.orfs() complete_orf = intervals.Interval(0, len(self) - 1) for orf in orfs: if orf == complete_orf: return True return False def looks_like_gene(self): '''Returns true iff: length >=6, length is a multiple of 3, first codon is start, last codon is a stop and has no other stop codons''' return self.is_complete_orf() \ and len(self) >= 6 \ and len(self) %3 == 0 \ and self.seq[0:3].upper() in genetic_codes.starts[genetic_code] def make_into_gene(self): '''Tries to make into a gene sequence. Tries all three reading frames and both strands. Returns a tuple (new sequence, strand, frame) if it was successful. Otherwise returns None.''' for reverse in [True, False]: for frame in range(3): new_seq = copy.copy(self) if reverse: new_seq.revcomp() new_seq.seq = new_seq[frame:] if len(new_seq) % 3: new_seq.seq = new_seq.seq[:-(len(new_seq) % 3)] new_aa_seq = new_seq.translate() if len(new_aa_seq) >= 2 and new_seq[0:3] in genetic_codes.starts[genetic_code] and new_aa_seq[-1] == '*' and '*' not in new_aa_seq[:-1]: strand = '-' if reverse else '+' return new_seq, strand, frame return None # Fills the object with the next sequence in the file. Returns # True if this was successful, False if no more sequences in the file. # If reading a file of quality scores, set read_quals = True def get_next_from_file(self, f, read_quals=False): if f in previous_lines: if previous_lines[f] == None: self.id = self.seq = None return False else: self.id = self._get_id_from_header_line(previous_lines[f]) else: line = '\n' while line == '\n': line = f.readline() self.id = self._get_id_from_header_line(line) self.seq = '' seq_lines = [] # much faster to store the seq lines in an array, # then join at the end while 1: line = f.readline() if line.startswith('>'): previous_lines[f] = line.rstrip() break elif line == '': previous_lines[f] = None break else: seq_lines.append(line.rstrip()) if read_quals: self.seq = ' '.join(seq_lines) else: self.seq = ''.join(seq_lines) return True def __str__(self): if Fasta.line_length == 0: return '>' + self.id + '\n' + self.seq else: return '>' + self.id + '\n' + '\n'.join(self.seq[i:i+Fasta.line_length] for i in range(0, len(self), Fasta.line_length)) def __getitem__(self, index): return self.seq[index] def trim(self, start, end): '''Removes first 'start'/'end' bases off the start/end of the sequence''' self.seq = self.seq[start:len(self.seq) - end] # qual_scores should be a list of quality scores def to_Fastq(self, qual_scores): '''Returns a Fastq object. qual_scores expected to be a list of numbers, like you would get in a .qual file''' if len(self) != len(qual_scores): raise Error('Error making Fastq from Fasta, lengths differ.', self.id) return Fastq(self.id, self.seq, ''.join([chr(max(0, min(x, 93)) + 33) for x in qual_scores])) def search(self, search_string): '''Finds every occurrence (including overlapping ones) of the search_string, including on the reverse strand. Returns a list where each element is a tuple (position, strand) where strand is in ['-', '+']. Positions are zero-based''' seq = self.seq.upper() search_string = search_string.upper() pos = 0 found = seq.find(search_string, pos) hits = [] while found != -1: hits.append((found, '+')) pos = found + 1 found = seq.find(search_string, pos) pos = 0 search_string = Fasta('x', search_string) search_string.revcomp() search_string = search_string.seq found = seq.find(search_string, pos) while found != -1: hits.append((found, '-')) pos = found + 1 found = seq.find(search_string, pos) return hits def translate(self, frame=0): '''Returns a Fasta sequence, translated into amino acids. Starts translating from 'frame', where frame expected to be 0,1 or 2''' return Fasta(self.id, ''.join([genetic_codes.codes[genetic_code].get(self.seq[x:x+3].upper(), 'X') for x in range(frame, len(self)-1-frame, 3)])) class Embl(Fasta): '''Exactly the same as Fasta, but reading seqs from a file works differently''' def __eq__(self, other): return type(other) in [Fasta, Embl] and type(self) in [Fasta, Embl] and self.__dict__ == other.__dict__ def _get_id_from_header_line(self, line): if line.startswith('ID ') and line[5] != ' ': return line.split()[1].rstrip(';') elif line.startswith('LOCUS'): return line.split()[1] else: raise Error('Error! expected line starting with "ID" or "LOCUS", but got this:\n', line) def get_next_from_file(self, f, read_quals=False): if f in previous_lines: line = '' if previous_lines[f] == None: self.id = self.seq = None return False else: self.id = self._get_id_from_header_line(previous_lines[f]) else: line = '\n' while line == '\n': line = f.readline() self.id = self._get_id_from_header_line(line) self.seq = '' seq_lines = [] while not (line.startswith('SQ') or line.rstrip() == 'ORIGIN'): line = f.readline() if line == '': raise Error('Error! No SQ or ORIGIN line found for sequence ' + self.id) line = f.readline() while not line.startswith('//'): if line == '' or line[0] != ' ': raise Error('Error! Did not find end of sequence ' + self.id) seq_lines.append(''.join(line.rstrip().strip(' 0123456789').split())) line = f.readline() while 1: if line.startswith('ID') or line.startswith('LOCUS'): previous_lines[f] = line.rstrip() break elif line == '': previous_lines[f] = None break line = f.readline() self.seq = ''.join(seq_lines) return True class Fastq(Fasta): '''Class to store and manipulate FASTQ sequences. They have three things: a name, sequence and string of quality scores''' def __init__(self, id_in=None, seq_in=None, qual_in=None): super().__init__(id_in, seq_in) self.qual = qual_in if (not self.seq == self.qual == None) and len(self.qual) != len(self.seq): raise Error('Error constructing Fastq. Mismatch in sequence and quality length\n' + str(self)) def __str__(self): return '@' + self.id + '\n' + self.seq + '\n+\n' + self.qual def __eq__(self, other): return type(other) is type(self) and self.__dict__ == other.__dict__ def subseq(self, start, end): '''Returns Fastq object with the same name, of the bases from start to end, but not including end''' return Fastq(self.id, self.seq[start:end], self.qual[start:end]) def get_next_from_file(self, f, read_quals=False): if f in previous_lines: line = previous_lines[f] del previous_lines[f] else: line = f.readline() while line == '\n': line = f.readline() if not line: self = Fastq('', '', '') return False if not line.startswith('@'): raise Error('Error getting next sequence from fastq file. Got line:\n' + line) self.id = line.rstrip()[1:] line = f.readline() if not line: raise Error('Error getting next sequence from fastq file, sequence has ID ' + self.id) self.seq = line.strip() line = f.readline() if not (line and line.startswith('+')): raise Error('Error getting next sequence from fastq file, no line starting with +, sequence has ID ' + self.id) line = f.readline() if not line: raise Error('Error getting next sequence from fastq file, sequence has ID ' + self.id) self.qual = line.rstrip() return True def revcomp(self): '''Reverse complements the sequence''' super().revcomp() self.qual = self.qual[::-1] def trim(self, start, end): '''Removes first 'start'/'end' bases off the start/end of the sequence''' super().trim(start, end) self.qual = self.qual[start:len(self.qual) - end] def to_Fasta_and_qual(self): quals = [ord(x) - 33 for x in self.qual] return (Fasta(self.id, self.seq), quals) def expand_nucleotides(self): return [Fastq(x.id, x.seq, self.qual) for x in super().expand_nucleotides()] def trim_Ns(self): '''Removes any leading or trailing N or n characters from the sequence''' # get index of first base that is not an N i = 0 while i < len(self) and self.seq[i] in 'nN': i += 1 # strip off start of sequence and quality self.seq = self.seq[i:] self.qual = self.qual[i:] # strip the ends self.seq = self.seq.rstrip('Nn') self.qual = self.qual[:len(self.seq)] def replace_interval(self, start, end, new, qual_string): '''Replaces the sequence from start to end with the sequence "new"''' if len(new) != len(qual_string): raise Error('Length of new seq and qual string in replace_interval() must be equal. Cannot continue') super().replace_interval(start, end, new) self.qual = self.qual[0:start] + qual_string + self.qual[end + 1:] def translate(self): '''Returns a Fasta sequence, translated into amino acids. Starts translating from 'frame', where frame expected to be 0,1 or 2''' fa = super().translate() return Fastq(fa.id, fa.seq, 'I'*len(fa.seq)) def make_into_gene(self): got = super().make_into_gene() if got is None: return None seq, strand, frame = got new_seq = copy.copy(self) if strand == '-': new_seq.revcomp() new_seq.seq = new_seq.seq[frame:frame + len(seq)] new_seq.qual = new_seq.qual[frame:frame + len(seq)] return new_seq, strand, frame def _orfs_from_aa_seq(seq): orfs = [] pos = 0 while pos < len(seq): next_stop = seq.find('*', pos) if next_stop == -1: orfs.append(intervals.Interval(pos, len(seq)-1)) break elif next_stop > pos: orfs.append(intervals.Interval(pos, next_stop)) pos = next_stop + 1 return orfs Fastaq-3.14.0/pyfastaq/tasks.py000066400000000000000000000676211276201573500163710ustar00rootroot00000000000000import re import sys import copy import random from pyfastaq import sequences, utils, caf class Error (Exception): pass def acgtn_only(infile, outfile): '''Replace every non-acgtn (case insensitve) character with an N''' f = utils.open_file_write(outfile) for seq in sequences.file_reader(infile): seq.replace_non_acgt() print(seq, file=f) utils.close(f) def caf_to_fastq(infile, outfile, min_length=0, trim=False): '''Convert a CAF file to fastq. Reads shorter than min_length are not output. If clipping information is in the CAF file (with a line Clipping QUAL ...) and trim=True, then trim the reads''' caf_reader = caf.file_reader(infile) fout = utils.open_file_write(outfile) for c in caf_reader: if trim: if c.clip_start is not None and c.clip_end is not None: c.seq.seq = c.seq.seq[c.clip_start:c.clip_end + 1] c.seq.qual = c.seq.qual[c.clip_start:c.clip_end + 1] else: print('Warning: no clipping info for sequence', c.id, file=sys.stderr) if len(c.seq) >= min_length: print(c.seq, file=fout) utils.close(fout) def capillary_to_pairs(infile, outprefix): # hash the sequences, only taking longest where an end has been sequenced more than once seq_reader = sequences.file_reader(infile) fwd_seqs = {} rev_seqs = {} unpaired_seqs = {} for seq in seq_reader: id_info = seq.split_capillary_id() if id_info['dir'] == 'fwd': seq.id = id_info['prefix'] + '/1' h = fwd_seqs elif id_info['dir'] == 'rev': seq.id = id_info['prefix'] + '/2' h = rev_seqs else: seq.id = id_info['prefix'] h = unpaired_seqs key = id_info['prefix'] if key not in h or len(h[key]) < len(seq): h[key] = copy.copy(seq) # write the output files f_pe = utils.open_file_write(outprefix + '.paired.gz') f_up = utils.open_file_write(outprefix + '.unpaired.gz') for id in fwd_seqs: if id in rev_seqs: print(fwd_seqs[id], file=f_pe) print(rev_seqs[id], file=f_pe) del rev_seqs[id] else: print(fwd_seqs[id], file=f_up) for seq in rev_seqs.values(): print(seq, file=f_up) for seq in unpaired_seqs.values(): print(seq, file=f_up) utils.close(f_pe) utils.close(f_up) def count_sequences(infile): '''Returns the number of sequences in a file''' seq_reader = sequences.file_reader(infile) n = 0 for seq in seq_reader: n += 1 return n def deinterleave(infile, outfile_1, outfile_2, fasta_out=False): seq_reader = sequences.file_reader(infile) f_1 = utils.open_file_write(outfile_1) f_2 = utils.open_file_write(outfile_2) for seq in seq_reader: if fasta_out: print(sequences.Fasta(seq.id, seq.seq), file=f_1) else: print(seq, file=f_1) try: next(seq_reader) except StopIteration: utils.close(f_1) utils.close(f_2) raise Error('Error getting mate for sequence. Cannot continue') if fasta_out: print(sequences.Fasta(seq.id, seq.seq), file=f_2) else: print(seq, file=f_2) utils.close(f_1) utils.close(f_2) def enumerate_names(infile, outfile, start_index=1, keep_illumina_suffix=False, rename_file=None, suffix=None): seq_reader = sequences.file_reader(infile) fout_seqs = utils.open_file_write(outfile) counter = start_index if keep_illumina_suffix: sequence_suffixes = ['/1', '/2'] else: sequence_suffixes = [] if rename_file is not None: fout_rename = utils.open_file_write(rename_file) print('#old\tnew', file=fout_rename) for seq in seq_reader: old_id = seq.id seq.id = str(counter) for suff in sequence_suffixes: if old_id.endswith(suff): seq.id += suff break if rename_file is not None: print(old_id, seq.id, sep='\t', file=fout_rename) if suffix is not None: seq.id += suffix print(seq, file=fout_seqs) counter += 1 utils.close(fout_seqs) if rename_file is not None: utils.close(fout_rename) def expand_nucleotides(infile, outfile): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: seqs = seq.expand_nucleotides() if len(seqs) > 1: for s in seqs: print(s, file=fout) else: print(seq, file=fout) def trim_contigs(infile, outfile, trim): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: if len(seq) < 2 * trim: continue gaps = seq.gaps() bases = list(seq.seq) # extend the length of each gap for gap in gaps: left_start = max(gap.start - trim, 0) right_end = min(gap.end + trim + 1, len(seq)) for i in range(left_start, gap.start): bases[i] = 'N' for i in range(gap.end, right_end): bases[i] = 'N' seq.seq = ''.join(bases) # trim start/end bases and tidy up any resulting Ns at either end of the trimmed seq seq.trim(trim, trim) seq.trim_Ns() # check that there is some non-N sequence left over regex = re.compile('[^nN]') if regex.search(seq.seq) is not None: print(seq, file=fout) utils.close(fout) def fastaq_to_fake_qual(infile, outfile, q=40): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: print('>' + seq.id, file=fout) if sequences.Fasta.line_length == 0: print(' '.join([str(q)] * len(seq)), file=fout) else: for i in range(0, len(seq), sequences.Fasta.line_length): print(' '.join([str(q)] * min(sequences.Fasta.line_length, len(seq) - i)), file=fout) utils.close(fout) def fasta_to_fastq(fasta_in, qual_in, outfile): fa_reader = sequences.file_reader(fasta_in) qual_reader = sequences.file_reader(qual_in, read_quals=True) f_out = utils.open_file_write(outfile) for seq in fa_reader: qual = next(qual_reader) if seq.id != qual.id: utils.close(f_out) raise Error('Mismatch in names from fasta and qual file', seq.id, qual.id) qual.seq = [int(x) for x in qual.seq.split()] print(seq.to_Fastq(qual.seq), file=f_out) utils.close(f_out) def fastaq_to_mira_xml(infile, outfile): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) print('', '', sep='\n', file=fout) for seq in seq_reader: print(' ', ' ' + seq.id + '', ' ' + str(len(seq)) + '', ' 1', ' ', sep='\n', file=fout) print('', file=fout) utils.close(fout) def fastaq_to_orfs_gff(infile, outfile, min_length=300, tool_name='fastaq'): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: orfs = seq.all_orfs(min_length=min_length) for coords, revcomp in orfs: if revcomp: strand = '-' else: strand = '+' print(seq.id, tool_name, 'CDS', coords.start+1, coords.end+1, '.', strand, '.', sep='\t', file=fout) utils.close(fout) def file_to_dict(infile, d): seq_reader = sequences.file_reader(infile) for seq in seq_reader: d[seq.id] = copy.copy(seq) def filter( infile, outfile, minlength=0, maxlength=float('inf'), regex=None, ids_file=None, invert=False, mate_in=None, mate_out=None, both_mates_pass=True, ): ids_from_file = set() if ids_file is not None: f = utils.open_file_read(ids_file) for line in f: ids_from_file.add(line.rstrip()) utils.close(f) if mate_in: if mate_out is None: raise Error('Error in filter! mate_in provided. Must also provide mate_out') seq_reader_mate = sequences.file_reader(mate_in) f_out_mate = utils.open_file_write(mate_out) seq_reader = sequences.file_reader(infile) f_out = utils.open_file_write(outfile) if regex is not None: r = re.compile(regex) def passes(seq): return minlength <= len(seq) <= maxlength \ and (regex is None or r.search(seq.id) is not None) \ and (ids_file is None or seq.id in ids_from_file) for seq in seq_reader: seq_passes = passes(seq) if mate_in: try: seq_mate = next(seq_reader_mate) except: utils.close(f_out) raise Error('Error getting mate for sequence', seq.id, ' ... cannot continue') mate_passes = passes(seq_mate) want_the_pair = (seq_passes and mate_passes) \ or (( seq_passes or mate_passes) and not both_mates_pass) if want_the_pair != invert: print(seq, file=f_out) print(seq_mate, file=f_out_mate) elif seq_passes != invert: print(seq, file=f_out) utils.close(f_out) if mate_in: utils.close(f_out_mate) def get_ids(infile, outfile): seq_reader = sequences.file_reader(infile) f_out = utils.open_file_write(outfile) for seq in seq_reader: print(seq.id, file=f_out) utils.close(f_out) def get_seqs_flanking_gaps(infile, outfile, left, right): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) print('#id', 'gap_start', 'gap_end', 'left_bases', 'right_bases', sep='\t', file=fout) for seq in seq_reader: gaps = seq.gaps() for gap in gaps: left_start = max(gap.start - left, 0) right_end = min(gap.end + right + 1, len(seq)) print(seq.id, gap.start + 1, gap.end + 1, seq.seq[left_start:gap.start], seq.seq[gap.end + 1:right_end], sep='\t', file=fout) utils.close(fout) def interleave(infile_1, infile_2, outfile, suffix1=None, suffix2=None): '''Makes interleaved file from two sequence files. If used, will append suffix1 onto end of every sequence name in infile_1, unless it already ends with suffix1. Similar for sufffix2.''' seq_reader_1 = sequences.file_reader(infile_1) seq_reader_2 = sequences.file_reader(infile_2) f_out = utils.open_file_write(outfile) for seq_1 in seq_reader_1: try: seq_2 = next(seq_reader_2) except: utils.close(f_out) raise Error('Error getting mate for sequence', seq_1.id, ' ... cannot continue') if suffix1 is not None and not seq_1.id.endswith(suffix1): seq_1.id += suffix1 if suffix2 is not None and not seq_2.id.endswith(suffix2): seq_2.id += suffix2 print(seq_1, file=f_out) print(seq_2, file=f_out) try: seq_2 = next(seq_reader_2) except: seq_2 = None if seq_2 is not None: utils.close(f_out) raise Error('Error getting mate for sequence', seq_2.id, ' ... cannot continue') utils.close(f_out) def make_random_contigs(contigs, length, outfile, name_by_letters=False, prefix='', seed=None, first_number=1): '''Makes a multi fasta file of random sequences, all the same length''' random.seed(a=seed) fout = utils.open_file_write(outfile) letters = list('ABCDEFGHIJKLMNOPQRSTUVWXYZ') letters_index = 0 for i in range(contigs): if name_by_letters: name = letters[letters_index] letters_index += 1 if letters_index == len(letters): letters_index = 0 else: name = str(i + first_number) fa = sequences.Fasta(prefix + name, ''.join([random.choice('ACGT') for x in range(length)])) print(fa, file=fout) utils.close(fout) def mean_length(infile, limit=None): '''Returns the mean length of the sequences in the input file. By default uses all sequences. To limit to the first N sequences, use limit=N''' total = 0 count = 0 seq_reader = sequences.file_reader(infile) for seq in seq_reader: total += len(seq) count += 1 if limit is not None and count >= limit: break assert count > 0 return total / count def merge_to_one_seq(infile, outfile, seqname='union'): '''Takes a multi fasta or fastq file and writes a new file that contains just one sequence, with the original sequences catted together, preserving their order''' seq_reader = sequences.file_reader(infile) seqs = [] for seq in seq_reader: seqs.append(copy.copy(seq)) new_seq = ''.join([seq.seq for seq in seqs]) if type(seqs[0]) == sequences.Fastq: new_qual = ''.join([seq.qual for seq in seqs]) seqs[:] = [] merged = sequences.Fastq(seqname, new_seq, new_qual) else: merged = sequences.Fasta(seqname, new_seq) seqs[:] = [] f = utils.open_file_write(outfile) print(merged, file=f) utils.close(f) def reverse_complement(infile, outfile): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: seq.revcomp() print(seq, file=fout) utils.close(fout) def scaffolds_to_contigs(infile, outfile, number_contigs=False): '''Makes a file of contigs from scaffolds by splitting at every N. Use number_contigs=True to add .1, .2, etc onto end of each contig, instead of default to append coordinates.''' seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: contigs = seq.contig_coords() counter = 1 for contig in contigs: if number_contigs: name = seq.id + '.' + str(counter) counter += 1 else: name = '.'.join([seq.id, str(contig.start + 1), str(contig.end + 1)]) print(sequences.Fasta(name, seq[contig.start:contig.end+1]), file=fout) utils.close(fout) def search_for_seq(infile, outfile, search_string): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: hits = seq.search(search_string) for hit in hits: print(seq.id, hit[0]+1, hit[1], sep='\t', file=fout) utils.close(fout) def sequence_trim(infile_1, infile_2, outfile_1, outfile_2, to_trim_file, min_length=50, check_revcomp=False): to_trim_seqs = {} file_to_dict(to_trim_file, to_trim_seqs) trim_seqs = [x.seq for x in to_trim_seqs.values()] if check_revcomp: for seq in to_trim_seqs.values(): seq.revcomp() trim_seqs_revcomp = [x.seq for x in to_trim_seqs.values()] else: trim_seqs_revcomp = [] seq_reader_1 = sequences.file_reader(infile_1) seq_reader_2 = sequences.file_reader(infile_2) f_out_1 = utils.open_file_write(outfile_1) f_out_2 = utils.open_file_write(outfile_2) for seq_1 in seq_reader_1: try: seq_2 = next(seq_reader_2) except: utils.close(f_out) raise Error('Error getting mate for sequence', seq_1.id, ' ... cannot continue') for seq in seq_1, seq_2: for trim_seq in trim_seqs: if seq.seq.startswith(trim_seq): seq.trim(len(trim_seq),0) break for trim_seq in trim_seqs_revcomp: if seq.seq.endswith(trim_seq): seq.trim(0,len(trim_seq)) break if len(seq_1) >= min_length and len(seq_2) >= min_length: print(seq_1, file=f_out_1) print(seq_2, file=f_out_2) utils.close(f_out_1) utils.close(f_out_2) def sort_by_size(infile, outfile, smallest_first=False): '''Sorts input sequence file by biggest sequence first, writes sorted output file. Set smallest_first=True to have smallest first''' seqs = {} file_to_dict(infile, seqs) seqs = list(seqs.values()) seqs.sort(key=lambda x: len(x), reverse=not smallest_first) fout = utils.open_file_write(outfile) for seq in seqs: print(seq, file=fout) utils.close(fout) def to_fastg(infile, outfile, circular=None): '''Writes a FASTG file in SPAdes format from input file. Currently only whether or not a sequence is circular is supported. Put circular=set of ids, or circular=filename to make those sequences circular in the output. Puts coverage=1 on all contigs''' if circular is None: to_circularise = set() elif type(circular) is not set: f = utils.open_file_read(circular) to_circularise = set([x.rstrip() for x in f.readlines()]) utils.close(f) else: to_circularise = circular seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) nodes = 1 for seq in seq_reader: new_id = '_'.join([ 'NODE', str(nodes), 'length', str(len(seq)), 'cov', '1', 'ID', seq.id ]) if seq.id in to_circularise: seq.id = new_id + ':' + new_id + ';' print(seq, file=fout) seq.revcomp() seq.id = new_id + "':" + new_id + "';" print(seq, file=fout) else: seq.id = new_id + ';' print(seq, file=fout) seq.revcomp() seq.id = new_id + "';" print(seq, file=fout) nodes += 1 utils.close(fout) def translate(infile, outfile, frame=0): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: print(seq.translate(frame=frame), file=fout) utils.close(fout) def trim(infile, outfile, start, end): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: seq.trim(start, end) if len(seq): print(seq, file=fout) utils.close(fout) def trim_Ns_at_end(infile, outfile): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: seq.trim_Ns() if len(seq): print(seq, file=fout) utils.close(fout) def lengths_from_fai(fai_file, d): f = utils.open_file_read(fai_file) for line in f: (id, length) = line.rstrip().split()[:2] d[id] = int(length) utils.close(f) def length_offsets_from_fai(fai_file): '''Returns a dictionary of positions of the start of each sequence, as if all the sequences were catted into one sequence. eg if file has three sequences, seq1 10bp, seq2 30bp, seq3 20bp, then the output would be: {'seq1': 0, 'seq2': 10, 'seq3': 40}''' positions = {} total_length = 0 f = utils.open_file_read(fai_file) for line in f: try: (name, length) = line.rstrip().split()[:2] length = int(length) except: raise Error('Error reading the following line of fai file ' + fai_file + '\n' + line) positions[name] = total_length total_length += length utils.close(f) return positions def split_by_base_count(infile, outfiles_prefix, max_bases, max_seqs=None): '''Splits a fasta/q file into separate files, file size determined by number of bases. Puts <= max_bases in each split file The exception is a single sequence >=max_bases is put in its own file. This does not split sequences. ''' seq_reader = sequences.file_reader(infile) base_count = 0 file_count = 1 seq_count = 0 fout = None if max_seqs is None: max_seqs = float('inf') for seq in seq_reader: if base_count == 0: fout = utils.open_file_write(outfiles_prefix + '.' + str(file_count)) file_count += 1 if base_count + len(seq) > max_bases or seq_count >= max_seqs: if base_count == 0: print(seq, file=fout) utils.close(fout) else: utils.close(fout) fout = utils.open_file_write(outfiles_prefix + '.' + str(file_count)) print(seq, file=fout) base_count = len(seq) file_count += 1 seq_count = 1 else: base_count += len(seq) seq_count += 1 print(seq, file=fout) utils.close(fout) def split_by_fixed_size(infile, outfiles_prefix, chunk_size, tolerance, skip_if_all_Ns=False): '''Splits fasta/q file into separate files, with up to (chunk_size + tolerance) bases in each file''' file_count = 1 coords = [] small_sequences = [] # sequences shorter than chunk_size seq_reader = sequences.file_reader(infile) f_coords = utils.open_file_write(outfiles_prefix + '.coords') for seq in seq_reader: if skip_if_all_Ns and seq.is_all_Ns(): continue if len(seq) < chunk_size: small_sequences.append(copy.copy(seq)) elif len(seq) <= chunk_size + tolerance: f = utils.open_file_write(outfiles_prefix + '.' + str(file_count)) print(seq, file=f) utils.close(f) file_count += 1 else: # make list of chunk coords chunks = [(x,x+chunk_size) for x in range(0, len(seq), chunk_size)] if chunks[-1][1] - 1 > len(seq): chunks[-1] = (chunks[-1][0], len(seq)) if len(chunks) > 1 and (chunks[-1][1] - chunks[-1][0]) <= tolerance: chunks[-2] = (chunks[-2][0], chunks[-1][1]) chunks.pop() # write one output file per chunk offset = 0 for chunk in chunks: if not(skip_if_all_Ns and seq.is_all_Ns(start=chunk[0], end=chunk[1]-1)): f = utils.open_file_write(outfiles_prefix + '.' + str(file_count)) chunk_id = seq.id + ':' + str(chunk[0]+1) + '-' + str(chunk[1]) print(sequences.Fasta(chunk_id, seq[chunk[0]:chunk[1]]), file=f) print(chunk_id, seq.id, offset, sep='\t', file=f_coords) utils.close(f) file_count += 1 offset += chunk[1] - chunk[0] # write files of small sequences if len(small_sequences): f = utils.open_file_write(outfiles_prefix + '.' + str(file_count)) file_count += 1 base_count = 0 for seq in small_sequences: if base_count > 0 and base_count + len(seq) > chunk_size + tolerance: utils.close(f) f = utils.open_file_write(outfiles_prefix + '.' + str(file_count)) file_count += 1 base_count = 0 print(seq, file=f) base_count += len(seq) utils.close(f) def split_by_fixed_size_onefile(infile, outfile, chunk_size, tolerance, skip_if_all_Ns=False): '''Splits each sequence in infile into chunks of fixed size, last chunk can be up to (chunk_size + tolerance) in length''' seq_reader = sequences.file_reader(infile) f_out = utils.open_file_write(outfile) for seq in seq_reader: for i in range(0, len(seq), chunk_size): if i + chunk_size + tolerance >= len(seq): end = len(seq) else: end = i + chunk_size subseq = seq.subseq(i, end) if not (skip_if_all_Ns and subseq.is_all_Ns()): subseq.id += '.' + str(i+1) + '_' + str(end) print(subseq, file=f_out) if end == len(seq): break utils.close(f_out) def replace_bases(infile, outfile, old, new): seq_reader = sequences.file_reader(infile) f_out = utils.open_file_write(outfile) for seq in seq_reader: seq.replace_bases(old, new) print(seq, file=f_out) utils.close(f_out) def strip_illumina_suffix(infile, outfile): seq_reader = sequences.file_reader(infile) f_out = utils.open_file_write(outfile) for seq in seq_reader: seq.strip_illumina_suffix() print(seq, file=f_out) utils.close(f_out) def stats_from_fai(infile): '''Returns dictionary of length stats from an fai file. Keys are: longest, shortest, mean, total_length, N50, number''' f = utils.open_file_read(infile) try: lengths = sorted([int(line.split('\t')[1]) for line in f], reverse=True) except: raise Error('Error getting lengths from fai file ' + infile) utils.close(f) stats = {} if len(lengths) > 0: stats['longest'] = max(lengths) stats['shortest'] = min(lengths) stats['total_length'] = sum(lengths) stats['mean'] = stats['total_length'] / len(lengths) stats['number'] = len(lengths) cumulative_length = 0 for length in lengths: cumulative_length += length if cumulative_length >= 0.5 * stats['total_length']: stats['N50'] = length break else: stats = {x: 0 for x in ('longest', 'shortest', 'mean', 'N50', 'total_length', 'number')} return stats def to_boulderio(infile, outfile): '''Converts input sequence file into a "Boulder-IO format", as used by primer3''' seq_reader = sequences.file_reader(infile) f_out = utils.open_file_write(outfile) for sequence in seq_reader: print("SEQUENCE_ID=" + sequence.id, file=f_out) print("SEQUENCE_TEMPLATE=" + sequence.seq, file=f_out) print("=", file=f_out) utils.close(f_out) def to_fasta(infile, outfile, line_length=60, strip_after_first_whitespace=False, check_unique=False): seq_reader = sequences.file_reader(infile) f_out = utils.open_file_write(outfile) original_line_length = sequences.Fasta.line_length sequences.Fasta.line_length = line_length if check_unique: used_names = {} for seq in seq_reader: if strip_after_first_whitespace: seq.strip_after_first_whitespace() if check_unique: used_names[seq.id] = used_names.get(seq.id, 0) + 1 if type(seq) == sequences.Fastq: print(sequences.Fasta(seq.id, seq.seq), file=f_out) else: print(seq, file=f_out) utils.close(f_out) sequences.Fasta.line_length = original_line_length if check_unique: all_unique = True for name, count in used_names.items(): if count > 1: print('Sequence name "' + name + '" not unique. Found', count, 'times', file=sys.stderr) all_unique = False if not all_unique: raise Error('Not all sequence names unique. Cannot continue') def to_fasta_union(infile, outfile, seqname='union'): seq_reader = sequences.file_reader(infile) new_seq = [] for seq in seq_reader: new_seq.append(seq.seq) f_out = utils.open_file_write(outfile) print(sequences.Fasta(seqname, ''.join(new_seq)), file=f_out) utils.close(f_out) def to_unique_by_id(infile, outfile): seq_reader = sequences.file_reader(infile) seqs = {} ids_in_order = [] # has the reads, keeping the longest one when we get the same # name more than once for seq in seq_reader: if len(seq) == 0: continue if seq.id not in seqs: seqs[seq.id] = copy.copy(seq) ids_in_order.append(seq.id) elif len(seqs[seq.id]) < len(seq): seqs[seq.id] = copy.copy(seq) # write the output f_out = utils.open_file_write(outfile) for id in ids_in_order: print(seqs[id], file=f_out) utils.close(f_out) Fastaq-3.14.0/pyfastaq/tests/000077500000000000000000000000001276201573500160205ustar00rootroot00000000000000Fastaq-3.14.0/pyfastaq/tests/caf_test.py000066400000000000000000000025051276201573500201640ustar00rootroot00000000000000#!/usr/bin/env python3 import os import unittest from pyfastaq import caf, utils, sequences modules_dir = os.path.dirname(os.path.abspath(caf.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class TestCaf(unittest.TestCase): def test_get_next_from_file(self): '''Test get_next_from_file()''' f_in = utils.open_file_read(os.path.join(data_dir, 'caf_test.caf')) c = caf.Caf() c.get_next_from_file(f_in) read = caf.Caf() read.id = 'read1.p1k' read.seq = sequences.Fasta(read.id, 'NACGTAN') read.seq = read.seq.to_Fastq([4, 24, 42, 43, 40, 30, 8]) read.insert_min = 2000 read.insert_max = 4000 read.ligation = '12345' read.clone = 'clone1' read.clip_start = 1 read.clip_end = 5 self.assertEqual(c, read) c.get_next_from_file(f_in) read = caf.Caf() read.id = 'read2.p1k' read.seq = sequences.Fasta(read.id, 'CGACGTT') read.seq = read.seq.to_Fastq([9, 9, 40, 41, 42, 42, 4]) read.insert_min = 2000 read.insert_max = 4000 read.ligation = '23456' read.clone = 'clone2' read.clip_start = None read.clip_end = None self.assertEqual(c, read) utils.close(f_in) if __name__ == '__main__': unittest.main() Fastaq-3.14.0/pyfastaq/tests/data/000077500000000000000000000000001276201573500167315ustar00rootroot00000000000000Fastaq-3.14.0/pyfastaq/tests/data/caf_test.caf000066400000000000000000000013421276201573500211740ustar00rootroot00000000000000 DNA : read1.p1k NACG TAN BaseQuality : read1.p1k 4 24 42 43 40 30 8 Sequence : read1.p1k Is_read SCF_File read1.p1kSCF Template read1 Insert_size 2000 4000 Ligation_no 12345 Primer Universal_primer Strand Forward Dye Dye_terminator Clone clone1 Seq_vec SVEC 1 15 puc19 Sequencing_vector "puc19" Clipping QUAL 2 6 ProcessStatus PASS Asped 2006-7-5 Unpadded Align_to_SCF 1 1272 1 1272 DNA : read2.p1k CG ACGTT BaseQuality : read2.p1k 9 9 40 41 42 42 4 Sequence : read2.p1k Is_read SCF_File read2.p1kSCF Template read2 Insert_size 2000 4000 Ligation_no 23456 Primer Universal_primer Strand Forward Dye Dye_terminator Clone clone2 Seq_vec SVEC 1 32 puc19 Sequencing_vector "puc19" ProcessStatus PASS Unpadded Align_to_SCF 1 1347 1 1347 Fastaq-3.14.0/pyfastaq/tests/data/caf_test.to_fastq.no_trim.min_length_0.fq000066400000000000000000000000721276201573500266770ustar00rootroot00000000000000@read1.p1k NACGTAN + %9KLI?) @read2.p1k CGACGTT + **IJKK% Fastaq-3.14.0/pyfastaq/tests/data/caf_test.to_fastq.trim.min_length_6.fq000066400000000000000000000000351276201573500262100ustar00rootroot00000000000000@read2.p1k CGACGTT + **IJKK% Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.embl000066400000000000000000000247111276201573500226310ustar00rootroot00000000000000ID seq1; SV 1; linear; mRNA; STD; PLN; 1859 BP. XX AC X56734; S46826; XX DT 12-SEP-1991 (Rel. 29, Created) DT 25-NOV-2005 (Rel. 85, Last updated, Version 11) XX DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase XX KW beta-glucosidase. XX OS Trifolium repens (white clover) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. XX RN [5] RP 1-1859 RX DOI; 10.1007/BF00039495. RX PUBMED; 1907511. RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; RT "Nucleotide and derived amino acid sequence of the cyanogenic RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; RL Plant Mol. Biol. 17(2):209-219(1991). XX RN [6] RP 1-1859 RA Hughes M.A.; RT ; RL Submitted (19-NOV-1990) to the INSDC. RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle RL Upon Tyne, NE2 4HH, UK XX DR EuropePMC; PMC99098; 11752244. XX FH Key Location/Qualifiers FH FT source 1..1859 FT /organism="Trifolium repens" FT /mol_type="mRNA" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /tissue_type="leaves" FT /db_xref="taxon:3899" FT mRNA 1..1859 FT /experiment="experimental evidence, no additional details FT recorded" FT CDS 14..1495 FT /product="beta-glucosidase" FT /EC_number="3.2.1.21" FT /note="non-cyanogenic" FT /db_xref="GOA:P26204" FT /db_xref="InterPro:IPR001360" FT /db_xref="InterPro:IPR013781" FT /db_xref="InterPro:IPR017853" FT /db_xref="InterPro:IPR018120" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" XX SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other; aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60 cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120 tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180 aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240 tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300 caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360 ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420 atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480 ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540 tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600 gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660 aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720 aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780 taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840 gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900 cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960 gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020 ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080 acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140 acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200 gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260 gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320 agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380 ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440 taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500 tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560 ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620 tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680 aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740 agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800 tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa 1859 // ID seq2; SV 1; linear; mRNA; STD; PLN; 1859 BP. XX AC X56734; S46826; XX DT 12-SEP-1991 (Rel. 29, Created) DT 25-NOV-2005 (Rel. 85, Last updated, Version 11) XX DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase XX KW beta-glucosidase. XX OS Trifolium repens (white clover) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. XX RN [5] RP 1-1859 RX DOI; 10.1007/BF00039495. RX PUBMED; 1907511. RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; RT "Nucleotide and derived amino acid sequence of the cyanogenic RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; RL Plant Mol. Biol. 17(2):209-219(1991). XX RN [6] RP 1-1859 RA Hughes M.A.; RT ; RL Submitted (19-NOV-1990) to the INSDC. RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle RL Upon Tyne, NE2 4HH, UK XX DR EuropePMC; PMC99098; 11752244. XX FH Key Location/Qualifiers FH FT source 1..1859 FT /organism="Trifolium repens" FT /mol_type="mRNA" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /tissue_type="leaves" FT /db_xref="taxon:3899" FT mRNA 1..1859 FT /experiment="experimental evidence, no additional details FT recorded" FT CDS 14..1495 FT /product="beta-glucosidase" FT /EC_number="3.2.1.21" FT /note="non-cyanogenic" FT /db_xref="GOA:P26204" FT /db_xref="InterPro:IPR001360" FT /db_xref="InterPro:IPR013781" FT /db_xref="InterPro:IPR017853" FT /db_xref="InterPro:IPR018120" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" XX SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other; aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60 cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120 tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180 aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240 tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300 caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360 ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420 atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480 ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540 tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600 gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660 aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720 aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780 taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840 gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900 cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960 gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020 ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080 acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140 acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200 gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260 gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320 agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380 ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440 taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500 tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560 ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620 tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680 aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740 agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800 tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa ccccccccc 1859 // Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.embl.bad000066400000000000000000000246151276201573500233610ustar00rootroot00000000000000ID seq1; SV 1; linear; mRNA; STD; PLN; 1859 BP. XX AC X56734; S46826; XX DT 12-SEP-1991 (Rel. 29, Created) DT 25-NOV-2005 (Rel. 85, Last updated, Version 11) XX DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase XX KW beta-glucosidase. XX OS Trifolium repens (white clover) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. XX RN [5] RP 1-1859 RX DOI; 10.1007/BF00039495. RX PUBMED; 1907511. RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; RT "Nucleotide and derived amino acid sequence of the cyanogenic RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; RL Plant Mol. Biol. 17(2):209-219(1991). XX RN [6] RP 1-1859 RA Hughes M.A.; RT ; RL Submitted (19-NOV-1990) to the INSDC. RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle RL Upon Tyne, NE2 4HH, UK XX DR EuropePMC; PMC99098; 11752244. XX FH Key Location/Qualifiers FH FT source 1..1859 FT /organism="Trifolium repens" FT /mol_type="mRNA" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /tissue_type="leaves" FT /db_xref="taxon:3899" FT mRNA 1..1859 FT /experiment="experimental evidence, no additional details FT recorded" FT CDS 14..1495 FT /product="beta-glucosidase" FT /EC_number="3.2.1.21" FT /note="non-cyanogenic" FT /db_xref="GOA:P26204" FT /db_xref="InterPro:IPR001360" FT /db_xref="InterPro:IPR013781" FT /db_xref="InterPro:IPR017853" FT /db_xref="InterPro:IPR018120" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" XX SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other; aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60 cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120 tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180 aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240 tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300 caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360 ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420 atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480 ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540 tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600 gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660 aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720 aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780 taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840 gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900 cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960 gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020 ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080 acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140 acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200 gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260 gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320 agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380 ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440 taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500 tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560 ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620 tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680 aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740 agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800 tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa 1859 // ID seq2; SV 1; linear; mRNA; STD; PLN; 1859 BP. XX AC X56734; S46826; XX DT 12-SEP-1991 (Rel. 29, Created) DT 25-NOV-2005 (Rel. 85, Last updated, Version 11) XX DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase XX KW beta-glucosidase. XX OS Trifolium repens (white clover) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. XX RN [5] RP 1-1859 RX DOI; 10.1007/BF00039495. RX PUBMED; 1907511. RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; RT "Nucleotide and derived amino acid sequence of the cyanogenic RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; RL Plant Mol. Biol. 17(2):209-219(1991). XX RN [6] RP 1-1859 RA Hughes M.A.; RT ; RL Submitted (19-NOV-1990) to the INSDC. RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle RL Upon Tyne, NE2 4HH, UK XX DR EuropePMC; PMC99098; 11752244. XX FH Key Location/Qualifiers FH FT source 1..1859 FT /organism="Trifolium repens" FT /mol_type="mRNA" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /tissue_type="leaves" FT /db_xref="taxon:3899" FT mRNA 1..1859 FT /experiment="experimental evidence, no additional details FT recorded" FT CDS 14..1495 FT /product="beta-glucosidase" FT /EC_number="3.2.1.21" FT /note="non-cyanogenic" FT /db_xref="GOA:P26204" FT /db_xref="InterPro:IPR001360" FT /db_xref="InterPro:IPR013781" FT /db_xref="InterPro:IPR017853" FT /db_xref="InterPro:IPR018120" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" XX aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60 cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120 tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180 aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240 tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300 caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360 ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420 atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480 ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540 tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600 gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660 aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720 aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780 taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840 gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900 cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960 gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020 ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080 acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140 acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200 gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260 gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320 agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380 ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440 taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500 tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560 ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620 tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680 aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740 agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800 tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa ccccccccc 1859 // Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.embl.bad2000066400000000000000000000247061276201573500234440ustar00rootroot00000000000000ID seq1; SV 1; linear; mRNA; STD; PLN; 1859 BP. XX AC X56734; S46826; XX DT 12-SEP-1991 (Rel. 29, Created) DT 25-NOV-2005 (Rel. 85, Last updated, Version 11) XX DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase XX KW beta-glucosidase. XX OS Trifolium repens (white clover) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. XX RN [5] RP 1-1859 RX DOI; 10.1007/BF00039495. RX PUBMED; 1907511. RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; RT "Nucleotide and derived amino acid sequence of the cyanogenic RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; RL Plant Mol. Biol. 17(2):209-219(1991). XX RN [6] RP 1-1859 RA Hughes M.A.; RT ; RL Submitted (19-NOV-1990) to the INSDC. RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle RL Upon Tyne, NE2 4HH, UK XX DR EuropePMC; PMC99098; 11752244. XX FH Key Location/Qualifiers FH FT source 1..1859 FT /organism="Trifolium repens" FT /mol_type="mRNA" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /tissue_type="leaves" FT /db_xref="taxon:3899" FT mRNA 1..1859 FT /experiment="experimental evidence, no additional details FT recorded" FT CDS 14..1495 FT /product="beta-glucosidase" FT /EC_number="3.2.1.21" FT /note="non-cyanogenic" FT /db_xref="GOA:P26204" FT /db_xref="InterPro:IPR001360" FT /db_xref="InterPro:IPR013781" FT /db_xref="InterPro:IPR017853" FT /db_xref="InterPro:IPR018120" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" XX SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other; aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60 cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120 tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180 aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240 tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300 caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360 ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420 atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480 ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540 tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600 gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660 aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720 aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780 taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840 gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900 cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960 gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020 ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080 acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140 acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200 gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260 gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320 agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380 ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440 taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500 tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560 ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620 tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680 aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740 agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800 tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa 1859 ID seq2; SV 1; linear; mRNA; STD; PLN; 1859 BP. XX AC X56734; S46826; XX DT 12-SEP-1991 (Rel. 29, Created) DT 25-NOV-2005 (Rel. 85, Last updated, Version 11) XX DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase XX KW beta-glucosidase. XX OS Trifolium repens (white clover) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. XX RN [5] RP 1-1859 RX DOI; 10.1007/BF00039495. RX PUBMED; 1907511. RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; RT "Nucleotide and derived amino acid sequence of the cyanogenic RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; RL Plant Mol. Biol. 17(2):209-219(1991). XX RN [6] RP 1-1859 RA Hughes M.A.; RT ; RL Submitted (19-NOV-1990) to the INSDC. RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle RL Upon Tyne, NE2 4HH, UK XX DR EuropePMC; PMC99098; 11752244. XX FH Key Location/Qualifiers FH FT source 1..1859 FT /organism="Trifolium repens" FT /mol_type="mRNA" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /tissue_type="leaves" FT /db_xref="taxon:3899" FT mRNA 1..1859 FT /experiment="experimental evidence, no additional details FT recorded" FT CDS 14..1495 FT /product="beta-glucosidase" FT /EC_number="3.2.1.21" FT /note="non-cyanogenic" FT /db_xref="GOA:P26204" FT /db_xref="InterPro:IPR001360" FT /db_xref="InterPro:IPR013781" FT /db_xref="InterPro:IPR017853" FT /db_xref="InterPro:IPR018120" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" XX SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other; aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60 cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120 tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180 aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240 tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300 caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360 ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420 atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480 ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540 tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600 gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660 aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720 aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780 taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840 gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900 cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960 gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020 ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080 acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140 acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200 gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260 gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320 agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380 ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440 taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500 tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560 ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620 tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680 aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740 agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800 tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa ccccccccc 1859 // Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.embl.to_fasta000066400000000000000000000073201276201573500244250ustar00rootroot00000000000000>seq1 aaacaaaccaaatatggattttattgtagccatatttgctctgtttgttattagctcatt cacaattacttccacaaatgcagttgaagcttctactcttcttgacataggtaacctgag tcggagcagttttcctcgtggcttcatctttggtgctggatcttcagcataccaatttga aggtgcagtaaacgaaggcggtagaggaccaagtatttgggataccttcacccataaata tccagaaaaaataagggatggaagcaatgcagacatcacggttgaccaatatcaccgcta caaggaagatgttgggattatgaaggatcaaaatatggattcgtatagattctcaatctc ttggccaagaatactcccaaagggaaagttgagcggaggcataaatcacgaaggaatcaa atattacaacaaccttatcaacgaactattggctaacggtatacaaccatttgtaactct ttttcattgggatcttccccaagtcttagaagatgagtatggtggtttcttaaactccgg tgtaataaatgattttcgagactatacggatctttgcttcaaggaatttggagatagagt gaggtattggagtactctaaatgagccatgggtgtttagcaattctggatatgcactagg aacaaatgcaccaggtcgatgttcggcctccaacgtggccaagcctggtgattctggaac aggaccttatatagttacacacaatcaaattcttgctcatgcagaagctgtacatgtgta taagactaaataccaggcatatcaaaagggaaagataggcataacgttggtatctaactg gttaatgccacttgatgataatagcataccagatataaaggctgccgagagatcacttga cttccaatttggattgtttatggaacaattaacaacaggagattattctaagagcatgcg gcgtatagttaaaaaccgattacctaagttctcaaaattcgaatcaagcctagtgaatgg ttcatttgattttattggtataaactattactcttctagttatattagcaatgccccttc acatggcaatgccaaacccagttactcaacaaatcctatgaccaatatttcatttgaaaa acatgggatacccttaggtccaagggctgcttcaatttggatatatgtttatccatatat gtttatccaagaggacttcgagatcttttgttacatattaaaaataaatataacaatcct gcaattttcaatcactgaaaatggtatgaatgaattcaacgatgcaacacttccagtaga agaagctcttttgaatacttacagaattgattactattaccgtcacttatactacattcg ttctgcaatcagggctggctcaaatgtgaagggtttttacgcatggtcatttttggactg taatgaatggtttgcaggctttactgttcgttttggattaaactttgtagattagaaaga tggattaaaaaggtaccctaagctttctgcccaatggtacaagaactttctcaaaagaaa ctagctagtattattaaaagaactttgtagtagattacagtacatcgtttgaagttgagt tggtgcacctaattaaataaaagaggttactcttaacatatttttaggccattcgttgtg aagttgttaggctgttatttctattatactatgttgtagtaataagtgcattgttgtacc agaagctatgatcataactataggttgatccttcatgtatcagtttgatgttgagaatac tttgaattaaaagtctttttttatttttttaaaaaaaaaaaaaaaaaaaaaaaaaaaaa >seq2 aaacaaaccaaatatggattttattgtagccatatttgctctgtttgttattagctcatt cacaattacttccacaaatgcagttgaagcttctactcttcttgacataggtaacctgag tcggagcagttttcctcgtggcttcatctttggtgctggatcttcagcataccaatttga aggtgcagtaaacgaaggcggtagaggaccaagtatttgggataccttcacccataaata tccagaaaaaataagggatggaagcaatgcagacatcacggttgaccaatatcaccgcta caaggaagatgttgggattatgaaggatcaaaatatggattcgtatagattctcaatctc ttggccaagaatactcccaaagggaaagttgagcggaggcataaatcacgaaggaatcaa atattacaacaaccttatcaacgaactattggctaacggtatacaaccatttgtaactct ttttcattgggatcttccccaagtcttagaagatgagtatggtggtttcttaaactccgg tgtaataaatgattttcgagactatacggatctttgcttcaaggaatttggagatagagt gaggtattggagtactctaaatgagccatgggtgtttagcaattctggatatgcactagg aacaaatgcaccaggtcgatgttcggcctccaacgtggccaagcctggtgattctggaac aggaccttatatagttacacacaatcaaattcttgctcatgcagaagctgtacatgtgta taagactaaataccaggcatatcaaaagggaaagataggcataacgttggtatctaactg gttaatgccacttgatgataatagcataccagatataaaggctgccgagagatcacttga cttccaatttggattgtttatggaacaattaacaacaggagattattctaagagcatgcg gcgtatagttaaaaaccgattacctaagttctcaaaattcgaatcaagcctagtgaatgg ttcatttgattttattggtataaactattactcttctagttatattagcaatgccccttc acatggcaatgccaaacccagttactcaacaaatcctatgaccaatatttcatttgaaaa acatgggatacccttaggtccaagggctgcttcaatttggatatatgtttatccatatat gtttatccaagaggacttcgagatcttttgttacatattaaaaataaatataacaatcct gcaattttcaatcactgaaaatggtatgaatgaattcaacgatgcaacacttccagtaga agaagctcttttgaatacttacagaattgattactattaccgtcacttatactacattcg ttctgcaatcagggctggctcaaatgtgaagggtttttacgcatggtcatttttggactg taatgaatggtttgcaggctttactgttcgttttggattaaactttgtagattagaaaga tggattaaaaaggtaccctaagctttctgcccaatggtacaagaactttctcaaaagaaa ctagctagtattattaaaagaactttgtagtagattacagtacatcgtttgaagttgagt tggtgcacctaattaaataaaagaggttactcttaacatatttttaggccattcgttgtg aagttgttaggctgttatttctattatactatgttgtagtaataagtgcattgttgtacc agaagctatgatcataactataggttgatccttcatgtatcagtttgatgttgagaatac tttgaattaaaagtctttttttatttttttaaaaaaaaaaaaaaaaaaaaccccccccc Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.fa000066400000000000000000000000571276201573500222750ustar00rootroot00000000000000>1 ACGTA >2 A C GT A >3 ACGTA >4 ACGTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.fa.ids000066400000000000000000000000101276201573500230400ustar00rootroot000000000000001 2 3 4 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.fa.qual000066400000000000000000000001221276201573500232270ustar00rootroot00000000000000>1 40 40 40 40 40 >2 40 40 40 40 40 >3 40 40 40 40 40 >4 40 40 40 40 40 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.fa.qual.bad000066400000000000000000000001221276201573500237540ustar00rootroot00000000000000>1 40 40 40 40 40 >3 40 40 40 40 40 >3 40 40 40 40 40 >4 40 40 40 40 40 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.fasta_to_fastq.fq000066400000000000000000000001041276201573500253030ustar00rootroot00000000000000@1 ACGTA + IIIII @2 ACGTA + IIIII @3 ACGTA + IIIII @4 ACGTA + IIIII Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.gbk000066400000000000000000000213341276201573500224530ustar00rootroot00000000000000LOCUS NAME1 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds. ACCESSION U49845 VERSION U49845.1 GI:1293613 KEYWORDS . SOURCE Saccharomyces cerevisiae (baker's yeast) ORGANISM Saccharomyces cerevisiae Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces. REFERENCE 1 (bases 1 to 5028) AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W. TITLE Cloning and sequence of REV7, a gene whose function is required for DNA damage-induced mutagenesis in Saccharomyces cerevisiae JOURNAL Yeast 10 (11), 1503-1509 (1994) PUBMED 7871890 REFERENCE 2 (bases 1 to 5028) AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M. TITLE Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein JOURNAL Genes Dev. 10 (7), 777-793 (1996) PUBMED 8846915 REFERENCE 3 (bases 1 to 5028) AUTHORS Roemer,T. TITLE Direct Submission JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New Haven, CT, USA FEATURES Location/Qualifiers source 1..5028 /organism="Saccharomyces cerevisiae" /db_xref="taxon:4932" /chromosome="IX" /map="9" CDS <1..206 /codon_start=3 /product="TCP1-beta" /protein_id="AAA98665.1" /db_xref="GI:1293614" /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA AEVLLRVDNIIRARPRTANRQHM" gene 687..3158 /gene="AXL2" CDS 687..3158 /gene="AXL2" /note="plasma membrane glycoprotein" /codon_start=1 /function="required for axial budding pattern of S. cerevisiae" /product="Axl2p" /protein_id="AAA98666.1" /db_xref="GI:1293615" /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL VDFSNKSNVNVGQVKDIHGRIPEML" gene complement(3300..4037) /gene="REV7" CDS complement(3300..4037) /gene="REV7" /codon_start=1 /product="Rev7p" /protein_id="AAA98667.1" /db_xref="GI:1293616" /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK LISGDDKILNGVYSQYEEGESIFGSLF" ORIGIN 1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg 61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct 121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa 181 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc // LOCUS NAME2 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds. ACCESSION U49845 VERSION U49845.1 GI:1293613 KEYWORDS . SOURCE Saccharomyces cerevisiae (baker's yeast) ORGANISM Saccharomyces cerevisiae Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces. REFERENCE 1 (bases 1 to 5028) AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W. TITLE Cloning and sequence of REV7, a gene whose function is required for DNA damage-induced mutagenesis in Saccharomyces cerevisiae JOURNAL Yeast 10 (11), 1503-1509 (1994) PUBMED 7871890 REFERENCE 2 (bases 1 to 5028) AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M. TITLE Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein JOURNAL Genes Dev. 10 (7), 777-793 (1996) PUBMED 8846915 REFERENCE 3 (bases 1 to 5028) AUTHORS Roemer,T. TITLE Direct Submission JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New Haven, CT, USA FEATURES Location/Qualifiers source 1..5028 /organism="Saccharomyces cerevisiae" /db_xref="taxon:4932" /chromosome="IX" /map="9" CDS <1..206 /codon_start=3 /product="TCP1-beta" /protein_id="AAA98665.1" /db_xref="GI:1293614" /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA AEVLLRVDNIIRARPRTANRQHM" gene 687..3158 /gene="AXL2" CDS 687..3158 /gene="AXL2" /note="plasma membrane glycoprotein" /codon_start=1 /function="required for axial budding pattern of S. cerevisiae" /product="Axl2p" /protein_id="AAA98666.1" /db_xref="GI:1293615" /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL VDFSNKSNVNVGQVKDIHGRIPEML" gene complement(3300..4037) /gene="REV7" CDS complement(3300..4037) /gene="REV7" /codon_start=1 /product="Rev7p" /protein_id="AAA98667.1" /db_xref="GI:1293616" /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK LISGDDKILNGVYSQYEEGESIFGSLF" ORIGIN 1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg 61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct 121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa 181 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgaaa // Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.gbk.to_fasta000066400000000000000000000007361276201573500242550ustar00rootroot00000000000000>NAME1 gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattg ccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagct ctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaa tgccatgactcagattctaattttaagctattcaatttctctttgatc >NAME2 gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattg ccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagct ctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaa tgccatgactcagattctaattttaagctattcaatttctctttgaaa Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.line_length3.fa000066400000000000000000000000501276201573500246400ustar00rootroot00000000000000>1 ACG TA >2 ACG TA >3 ACG TA >4 ACG TA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_non_unique.in.fa000066400000000000000000000000401276201573500334660ustar00rootroot00000000000000>1 spam ACGT >1 eggs A >2 GTTTG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_non_unique.out.fa000066400000000000000000000000261276201573500336730ustar00rootroot00000000000000>1 ACGT >1 A >2 GTTTG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_unique.in.fa000066400000000000000000000000511276201573500326160ustar00rootroot00000000000000>1 abcde ACGT >2 abcde G >3 hello GTACCA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_unique.out.fa000066400000000000000000000000271276201573500330220ustar00rootroot00000000000000>1 ACGT >2 G >3 GTACCA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_3-per-line.fa000066400000000000000000000001041276201573500242210ustar00rootroot00000000000000>ID A >ID AA >ID AAA >ID AAA A >ID AAA AA >ID AAA AAA >ID AAA AAA A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_cap_to_read_pairs.fa000066400000000000000000000001511276201573500260060ustar00rootroot00000000000000>one.p1k ACGT >one.q1k CCCC >two.p1k A >two.q1k C >one.p1k TTTTTTTTTT >three.q1k A >four.x T >five.p1k G Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_cap_to_read_pairs.fa.paired.gz000066400000000000000000000001341276201573500276710ustar00rootroot00000000000000‹I0&Rsequences_test_cap_to_read_pairs.fa.pairs³ËÏKÕ7ä .;ˆ—3pÙ•”çe!   ]•’K0Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_cap_to_read_pairs.fa.unpaired.gz000066400000000000000000000001341276201573500302340ustar00rootroot00000000000000‹Ü3&Rsequences_test_cap_to_read_pairs.fa.unpaired³+É(JMÕ7ârä²KË/-â Ò™e©ú†\î\/zÔ0Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_deinterleaved_1.fa000066400000000000000000000000221276201573500254000ustar00rootroot00000000000000>1/1 ACGTA >2/1 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_deinterleaved_2.fa000066400000000000000000000000221276201573500254010ustar00rootroot00000000000000>1/2 ACGTA >2/2 C Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_deinterleaved_bad2_1.fa000066400000000000000000000000131276201573500262700ustar00rootroot00000000000000>1/1 ACGTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_deinterleaved_bad2_2.fa000066400000000000000000000000221276201573500262710ustar00rootroot00000000000000>1/2 ACGTA >2/2 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_deinterleaved_bad_1.fa000066400000000000000000000000221276201573500262060ustar00rootroot00000000000000>1/1 ACGTA >2/1 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_deinterleaved_bad_2.fa000066400000000000000000000000131276201573500262070ustar00rootroot00000000000000>1/2 ACGTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_1.fa000066400000000000000000000000201276201573500300060ustar00rootroot00000000000000>1/1 ACGTA >2 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_2.fa000066400000000000000000000000201276201573500300070ustar00rootroot00000000000000>1 ACGTA >2/2 C Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_empty_file000066400000000000000000000000001276201573500241110ustar00rootroot00000000000000Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_enumerate_names.fa000066400000000000000000000000441276201573500255210ustar00rootroot00000000000000>one/1 A >one/2 C >two/1 G >two/2 T Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.add_suffix000066400000000000000000000000601276201573500304400ustar00rootroot00000000000000>1.SUFFIX A >2.SUFFIX C >3.SUFFIX G >4.SUFFIX T Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.keep_suffix000066400000000000000000000000341276201573500306350ustar00rootroot00000000000000>1/1 A >2/2 C >3/1 G >4/2 T Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.start.1000066400000000000000000000000241276201573500276200ustar00rootroot00000000000000>1 A >2 C >3 G >4 T Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.start.1.rename_file000066400000000000000000000000511276201573500320650ustar00rootroot00000000000000#old new one/1 1 one/2 2 two/1 3 two/2 4 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_enumerate_names.fa.out.start.2000066400000000000000000000000241276201573500276210ustar00rootroot00000000000000>2 A >3 C >4 G >5 T Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_fai_test.fa000066400000000000000000000000321276201573500241440ustar00rootroot00000000000000>1 A >2 AA >3 AAA >4 AAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_fai_test.fa.fai000066400000000000000000000000521276201573500247040ustar00rootroot000000000000001 1 3 1 2 2 2 8 2 3 3 3 14 3 4 4 4 21 4 5 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_fail_no_AT.fq000066400000000000000000000000271276201573500243650ustar00rootroot00000000000000@1 A + I NOT_AN_@_LINE Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_fail_no_plus.fq000066400000000000000000000000171276201573500250430ustar00rootroot00000000000000@A A NOT_A_+ I Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_fail_no_qual.fq000066400000000000000000000000071276201573500250210ustar00rootroot00000000000000@A A + Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_fail_no_seq.fq000066400000000000000000000000141276201573500246450ustar00rootroot00000000000000@A A + I @B Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_fastaq_replace_bases.expected.fa000066400000000000000000000000151276201573500302760ustar00rootroot00000000000000>1 ACGXXXAXA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_fastaq_replace_bases.fa000066400000000000000000000000151276201573500264760ustar00rootroot00000000000000>1 ACGTTTATA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_filter_by_ids_file.fa000066400000000000000000000000401276201573500261620ustar00rootroot00000000000000>seq1 A >seq2 C >seq3 G >seq4 T Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_filter_by_ids_file.fa.filtered000066400000000000000000000000201276201573500277550ustar00rootroot00000000000000>seq2 C >seq4 T Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_filter_by_ids_file.fa.filtered.invert000066400000000000000000000000201276201573500312630ustar00rootroot00000000000000>seq1 A >seq3 G Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_filter_by_ids_file.fa.ids000066400000000000000000000000121276201573500267370ustar00rootroot00000000000000seq4 seq2 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_filter_by_regex.fa000066400000000000000000000000511276201573500255200ustar00rootroot00000000000000>1 AAA >a AAA >a/1 AAA >a/2 AAA >b/1 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_filter_by_regex.first-char-a.fa000066400000000000000000000000311276201573500277750ustar00rootroot00000000000000>a AAA >a/1 AAA >a/2 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_filter_by_regex.first-of-pair.fa000066400000000000000000000000221276201573500301770ustar00rootroot00000000000000>a/1 AAA >b/1 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_filter_by_regex.numeric.fa000066400000000000000000000000071276201573500271620ustar00rootroot00000000000000>1 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_get_seqs_flanking_gaps.fa000066400000000000000000000000401276201573500270420ustar00rootroot00000000000000>a ACGTCNGTCNNNGT >b ACGTGTGTTG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_get_seqs_flanking_gaps.fa.out000066400000000000000000000001121276201573500276500ustar00rootroot00000000000000#id gap_start gap_end left_bases right_bases a 6 6 GTC GTC a 10 12 GTC GT Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_gffv3.gff000066400000000000000000000002131276201573500235360ustar00rootroot00000000000000##gff-version 3 # comment ##sequence-region seq1 1 10 seq1 . gene 3 7 . + . ID=gene1;name=name1 ##FASTA >seq1 ACGTACGTAC >seq2 ACGTACGTAC Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_gffv3.gff.fasta000066400000000000000000000000421276201573500246330ustar00rootroot00000000000000>seq1 ACACGTGACG >seq2 AGTACCGTAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_gffv3.gff.to_fasta000066400000000000000000000000421276201573500253350ustar00rootroot00000000000000>seq1 ACGTACGTAC >seq2 ACGTACGTAC Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_gffv3.no_FASTA_line.gff000066400000000000000000000002031276201573500260750ustar00rootroot00000000000000##gff-version 3 # comment ##sequence-region seq1 1 10 seq1 . gene 3 7 . + . ID=gene1;name=name1 >seq1 ACGTACGTAC >seq2 ACGTACGTAC Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_gffv3.no_FASTA_line.gff.to_fasta000066400000000000000000000000421276201573500276750ustar00rootroot00000000000000>seq1 ACGTACGTAC >seq2 ACGTACGTAC Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_gffv3.no_seq.2.gff000066400000000000000000000001561276201573500251670ustar00rootroot00000000000000##gff-version 3 # comment ##sequence-region seq1 1 10 seq1 . gene 3 7 . + . ID=gene1;name=name1 ##FASTA oops Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_gffv3.no_seq.gff000066400000000000000000000001411276201573500250210ustar00rootroot00000000000000##gff-version 3 # comment ##sequence-region seq1 1 10 seq1 . gene 3 7 . + . ID=gene1;name=name1 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_good_file.fq000066400000000000000000000000531276201573500243200ustar00rootroot00000000000000@ID ACGTA + IIIII @ID ACGTA +blah IIIII Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_good_file.fq.to_fasta000066400000000000000000000000241276201573500261150ustar00rootroot00000000000000>ID ACGTA >ID ACGTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_good_file_mira.xml000066400000000000000000000005631276201573500255300ustar00rootroot00000000000000 ID 5 1 ID 5 1 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_interleaved.fa000066400000000000000000000000441276201573500246530ustar00rootroot00000000000000>1/1 ACGTA >1/2 ACGTA >2/1 A >2/2 C Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_interleaved.fq000066400000000000000000000000741276201573500246760ustar00rootroot00000000000000@1/1 ACGTA + IIIII @1/2 ACGTA + IIIII @2/1 A + I @2/2 C + I Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_interleaved_bad.fa000066400000000000000000000000351276201573500254610ustar00rootroot00000000000000>1/1 ACGTA >1/2 ACGTA >2/1 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_interleaved_with_suffixes.fa000066400000000000000000000000441276201573500276220ustar00rootroot00000000000000>1/1 ACGTA >1/2 ACGTA >2/1 A >2/2 C Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_length_filter.fa000066400000000000000000000000301276201573500251720ustar00rootroot00000000000000>3 AAA >4 AAAA >5 AAAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_length_filter.min-0.max-1.fa000066400000000000000000000000001276201573500270300ustar00rootroot00000000000000Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_length_filter.min-0.max-inf.fa000066400000000000000000000000301276201573500274470ustar00rootroot00000000000000>3 AAA >4 AAAA >5 AAAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_length_filter.min-4.max-4.fa000066400000000000000000000000101276201573500270400ustar00rootroot00000000000000>4 AAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_make_random_contigs.default.fa000066400000000000000000000000161276201573500277760ustar00rootroot00000000000000>1 ACG >2 ACG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_make_random_contigs.first-42.fa000066400000000000000000000000201276201573500277170ustar00rootroot00000000000000>42 ACG >43 ACG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_make_random_contigs.name-by-letters.fa000066400000000000000000000003041276201573500313620ustar00rootroot00000000000000>A ACG >B ACG >C ACG >D ACG >E ACG >F ACG >G ACG >H ACG >I ACG >J ACG >K ACG >L ACG >M ACG >N ACG >O ACG >P ACG >Q ACG >R ACG >S ACG >T ACG >U ACG >V ACG >W ACG >X ACG >Y ACG >Z ACG >A ACG >B ACG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_make_random_contigs.prefix-p.fa000066400000000000000000000000201276201573500300770ustar00rootroot00000000000000>p1 ACG >p2 ACG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_merge_to_one_seq.fa000066400000000000000000000000241276201573500256610ustar00rootroot00000000000000>1 A >2 G >3 C >4 T Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_merge_to_one_seq.fq000066400000000000000000000000221276201573500256770ustar00rootroot00000000000000@1 A + I @2 G + H Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_merge_to_one_seq.merged.fa000066400000000000000000000000141276201573500271220ustar00rootroot00000000000000>union AGCT Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_merge_to_one_seq.merged.fq000066400000000000000000000000171276201573500271450ustar00rootroot00000000000000@union AG + IH Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_not_a_fastaq_file000066400000000000000000000000371276201573500254240ustar00rootroot00000000000000i am not a fasta or fastq file Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_one-per-line.fa000066400000000000000000000000771276201573500246510ustar00rootroot00000000000000>ID A >ID AA >ID AAA >ID AAAA >ID AAAAA >ID AAAAAA >ID AAAAAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_orfs.fa000066400000000000000000000017741276201573500233350ustar00rootroot00000000000000>1 GTATGACGACTTCTCGGTCAAAGGTAAGGTGAACAAGGGATTGAATGCTTAAATCCCGTG CCTACACTCAGTACCGGTGCTTGGCTGAAGCGTTCCTATGCAAGAATGAGAACTGGCAAC ACGTCGCGGCCAGCCCGGGACCATCAGGACCCGAACGTGTACCGCGAATGTTTACATTTC ACCCAGTTACCCGGATTCGGGCCAAAGCAGGAGAGCCTCTGAATTAGATGGTGCCACGTA AGTCTATTTTCGCACGTTTTATTGATTCAAGTGAGTGTCAACGTAGATTTATTGGTGCTT GGCTAAAGACGTATGGATCACGGGATGGAACATCTGGATCCCCCATGTACGTAAGTGTGT CGTCAAACAAAATTCTGTATCCCGTCGCTCCTGCCAGGGCAATCGCGGAGCTACGGACAT AGTCCTTAGTGAACTAATGATGATGAACATCTCGAACCAGGTTAACACGATACGATGAAG CGGGTTACTGAACACACTTAACAGGAGCCTGAGCAAATGTCATTTACAAAAGGTTTCTAG ACCCCCTTGGTAAGTCACTTGACACGTCTCATGCGGGGCCTACGGTAAACCAGATGCTAG AGTAGCGAACGGTGGGTGCGCAGGCATGTCCGGTCTCTCGATGGTGCACTTACGGACATC TCCCTATACAGATCTATTCAGTCACGAAGGTCAGCGAACATAACCCACGGGAGTTATCTC AACGAGTACGGGAGCGAACGGTGCACGGATCTGTCTTAGCTCAGAGGCGTCACGCGGTCC TATCTAACGCAAGAGCATGTGCCATTCCGGCCCTCTGATGTGCCTATGTACATAGAGCCG ACCCCGGCGGATTGGAGTCCCTAGCTACCGTCGACAGAGACGCAAAGACTCAATTGCTAT GTATATTGTTACTCTTCAACCACTGGAAAGACAAATAATTGCGGGCAAGTGCGTTACCCA TCACTCTGTTCTGTACACGAAAGGCTGAATAGCAAGTGGC Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_orfs.gff000066400000000000000000000006221276201573500235000ustar00rootroot000000000000001 fastaq CDS 28 222 . + . 1 fastaq CDS 45 227 . + . 1 fastaq CDS 49 171 . - . 1 fastaq CDS 110 241 . + . 1 fastaq CDS 144 266 . - . 1 fastaq CDS 228 422 . + . 1 fastaq CDS 278 433 . - . 1 fastaq CDS 287 478 . + . 1 fastaq CDS 289 519 . - . 1 fastaq CDS 563 703 . + . 1 fastaq CDS 601 759 . + . 1 fastaq CDS 606 818 . + . 1 fastaq CDS 819 938 . + . 1 fastaq CDS 836 988 . + . 1 fastaq CDS 865 999 . + . Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_phylip.interleaved000066400000000000000000000002661276201573500256000ustar00rootroot00000000000000 3 42 Turkey AA-CTNGGGC ATTTCAGGGT Salmo_gairAAGCCTTGGC AGTGCAGGGT H. SapiensACCGGTTGGC CGTTCAGGGT GAGCCCGGGC AATACAGGGT AT GAGCCGTGGC CGGGCACGGT AT ACAGGTTGGC CGTTCAGGGT AA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_phylip.interleaved.to_fasta000066400000000000000000000002401276201573500273670ustar00rootroot00000000000000>Turkey AACTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT >Salmo_gair AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT >H. Sapiens ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_phylip.interleaved2000066400000000000000000000002651276201573500256610ustar00rootroot00000000000000 3 42 Turkey AA-CTNGGGC ATTTCAGGGT Salmo_gairAAGCCTTGGC AGTGCAGGGT H. SapiensACCGGTTGGC CGTTCAGGGT GAGCCCGGGC AATACAGGGT AT GAGCCGTGGC CGGGCACGGT AT ACAGGTTGGC CGTTCAGGGT AA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_phylip.interleaved2.to_fasta000066400000000000000000000002401276201573500274510ustar00rootroot00000000000000>Turkey AACTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT >Salmo_gair AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT >H. Sapiens ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_phylip.made_by_seaview000066400000000000000000000004161276201573500264160ustar00rootroot000000000000002 97 seq1 GGGGGGGGGG GGGGGGGGGG GGGGGGGGGG GGGGGGGGGG GGGGGGGGGG GGGGGGGGGG seq2 AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA GGGGGGGGGG GGGGGGGGGG GGGGGGGGGG GGGGGGT AAAAAAAAAA AAAAAAAAAA AAAAAAAAA- -AAAAAG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_phylip.made_by_seaview.to_fasta000066400000000000000000000003201276201573500302070ustar00rootroot00000000000000>seq1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGT >seq2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_phylip.sequential000066400000000000000000000002651276201573500254470ustar00rootroot00000000000000 3 42 Turkey AA-CTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT Salmo_gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_phylip.sequential.to_fasta000066400000000000000000000002401276201573500272370ustar00rootroot00000000000000>Turkey AACTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT >Salmo_gair AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT >H. Sapiens ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_revcomp.fa000066400000000000000000000000441276201573500240240ustar00rootroot00000000000000>1 TACGT >2 TACGT >3 TACGT >4 TACGT Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_search_string.fa000066400000000000000000000000241276201573500252020ustar00rootroot00000000000000>seq AAGATCTAGAGATC Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_search_string.fa.hits000066400000000000000000000000411276201573500261470ustar00rootroot00000000000000seq 2 + seq 8 + seq 10 + seq 5 - Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa000066400000000000000000000001021276201573500257100ustar00rootroot00000000000000>seq1 ACGTNNNNN >seq2 ACGTA >seq3 NNNN >seq4 AC >seq5 ACG >seq6 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.1000066400000000000000000000000171276201573500272060ustar00rootroot00000000000000>seq1:1-4 ACGT Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.2000066400000000000000000000000201276201573500272010ustar00rootroot00000000000000>seq1:5-9 NNNNN Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.3000066400000000000000000000000141276201573500272050ustar00rootroot00000000000000>seq2 ACGTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.4000066400000000000000000000000131276201573500272050ustar00rootroot00000000000000>seq3 NNNN Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.5000066400000000000000000000000231276201573500272070ustar00rootroot00000000000000>seq4 AC >seq5 ACG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.6000066400000000000000000000000101276201573500272040ustar00rootroot00000000000000>seq6 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.coords000066400000000000000000000000401276201573500303330ustar00rootroot00000000000000seq1:1-4 seq1 0 seq1:5-9 seq1 4 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.1000066400000000000000000000000171276201573500321210ustar00rootroot00000000000000>seq1:1-4 ACGT Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.2000066400000000000000000000000141276201573500321170ustar00rootroot00000000000000>seq2 ACGTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.3000066400000000000000000000000231276201573500321200ustar00rootroot00000000000000>seq4 AC >seq5 ACG Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.4000066400000000000000000000000101276201573500321150ustar00rootroot00000000000000>seq6 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords000066400000000000000000000000201276201573500332440ustar00rootroot00000000000000seq1:1-4 seq1 0 Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.fa000066400000000000000000000001541276201573500274200ustar00rootroot00000000000000>seq1 A >seq2 NC >seq3 ACG >seq4 ACGT >seq5 NNNTA >seq6 ACGTAC >seq7 ACGTACG >seq8 ACGTACGT >seq9 ACGTACGTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.out.fa000066400000000000000000000003351276201573500302270ustar00rootroot00000000000000>seq1.1_1 A >seq2.1_2 NC >seq3.1_3 ACG >seq4.1_4 ACGT >seq5.1_3 NNN >seq5.4_5 TA >seq6.1_3 ACG >seq6.4_6 TAC >seq7.1_3 ACG >seq7.4_7 TACG >seq8.1_3 ACG >seq8.4_6 TAC >seq8.7_8 GT >seq9.1_3 ACG >seq9.4_6 TAC >seq9.7_9 GTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_fixed_size_onefile.skip_Ns.out.fa000066400000000000000000000003171276201573500316340ustar00rootroot00000000000000>seq1.1_1 A >seq2.1_2 NC >seq3.1_3 ACG >seq4.1_4 ACGT >seq5.4_5 TA >seq6.1_3 ACG >seq6.4_6 TAC >seq7.1_3 ACG >seq7.4_7 TACG >seq8.1_3 ACG >seq8.4_6 TAC >seq8.7_8 GT >seq9.1_3 ACG >seq9.4_6 TAC >seq9.7_9 GTA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa000066400000000000000000000000321276201573500245400ustar00rootroot00000000000000>1 A >2 AA >3 AAA >4 AAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.2.1000066400000000000000000000000051276201573500250370ustar00rootroot00000000000000>1 A Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.2.2000066400000000000000000000000061276201573500250410ustar00rootroot00000000000000>2 AA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.2.3000066400000000000000000000000071276201573500250430ustar00rootroot00000000000000>3 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.2.4000066400000000000000000000000101276201573500250360ustar00rootroot00000000000000>4 AAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.3.1000066400000000000000000000000131276201573500250370ustar00rootroot00000000000000>1 A >2 AA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.3.2000066400000000000000000000000071276201573500250430ustar00rootroot00000000000000>3 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.3.3000066400000000000000000000000101276201573500250360ustar00rootroot00000000000000>4 AAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.4.1000066400000000000000000000000131276201573500250400ustar00rootroot00000000000000>1 A >2 AA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.4.2000066400000000000000000000000071276201573500250440ustar00rootroot00000000000000>3 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.4.3000066400000000000000000000000101276201573500250370ustar00rootroot00000000000000>4 AAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.6.1000066400000000000000000000000221276201573500250420ustar00rootroot00000000000000>1 A >2 AA >3 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.6.2000066400000000000000000000000101276201573500250400ustar00rootroot00000000000000>4 AAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.6.limit2.1000066400000000000000000000000131276201573500262410ustar00rootroot00000000000000>1 A >2 AA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.6.limit2.2000066400000000000000000000000071276201573500262450ustar00rootroot00000000000000>3 AAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.fa.6.limit2.3000066400000000000000000000000101276201573500262400ustar00rootroot00000000000000>4 AAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.long.fa000066400000000000000000000000301276201573500254740ustar00rootroot00000000000000>1 AAAAAAAA >2 AAAAAAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.long.fa.2.1000066400000000000000000000000141276201573500257750ustar00rootroot00000000000000>1 AAAAAAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_split_test.long.fa.2.2000066400000000000000000000000141276201573500257760ustar00rootroot00000000000000>2 AAAAAAAA Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_strip_after_whitespace.fa000066400000000000000000000000441276201573500271070ustar00rootroot00000000000000>seq 1 ACGT >seq 1 2 ACGT >seq ACGT Fastaq-3.14.0/pyfastaq/tests/data/sequences_test_strip_after_whitespace.fa.to_fasta000066400000000000000000000000361276201573500307070ustar00rootroot00000000000000>seq ACGT >seq ACGT >seq ACGT 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>12/2 AACG1234567890CGTT Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_sequence_trim_2.trimmed.fa000066400000000000000000000001411276201573500262250ustar00rootroot00000000000000>1/2 1234567890 >4/2 1234567890 >5/2 1234567890 >6/2 1234567890 >9/2 1234567890 >12/2 1234567890 Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_sequences_to_trim.fa000066400000000000000000000000201276201573500252250ustar00rootroot00000000000000>1 AACG >2 GCCT Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_sort_by_size.in.fa000066400000000000000000000000371276201573500246250ustar00rootroot00000000000000>1 AGTCA >2 ACGTTT >3 A >4 ACG Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_sort_by_size.out.fa000066400000000000000000000000371276201573500250260ustar00rootroot00000000000000>2 ACGTTT >1 AGTCA >4 ACG >3 A Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_sort_by_size.out.rev.fa000066400000000000000000000000371276201573500256210ustar00rootroot00000000000000>3 A >4 ACG >1 AGTCA >2 ACGTTT Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_stats_from_fai.in.empty.fai000066400000000000000000000000001276201573500264060ustar00rootroot00000000000000Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_stats_from_fai.in.fai000066400000000000000000000001101276201573500252530ustar00rootroot00000000000000seq1 3 6 3 4 seq2 4 16 4 5 seq3 10 27 10 11 seq4 3 44 3 4 seq5 1 54 1 2 Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_to_boulderio.in.fa000066400000000000000000000001461276201573500246010ustar00rootroot00000000000000>one ACGTCAGCTCTGATCGACTGATGCACTAATCATATCTCGATCGATCGATCTGACTGACT CAGACCTCATACTACTTGCTGATAAT >two TGCA Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_to_boulderio.out.boulder000066400000000000000000000002431276201573500260460ustar00rootroot00000000000000SEQUENCE_ID=one SEQUENCE_TEMPLATE=ACGTCAGCTCTGATCGACTGATGCACTAATCATATCTCGATCGATCGATCTGACTGACTCAGACCTCATACTACTTGCTGATAAT = SEQUENCE_ID=two SEQUENCE_TEMPLATE=TGCA = Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_to_fastg.fasta000066400000000000000000000000271276201573500240220ustar00rootroot00000000000000>seq1 ATTTG >seq2 ACCG Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_to_fastg.fastg000066400000000000000000000003251276201573500240310ustar00rootroot00000000000000>NODE_1_length_5_cov_1_ID_seq1; ATTTG >NODE_1_length_5_cov_1_ID_seq1'; CAAAT >NODE_2_length_4_cov_1_ID_seq2:NODE_2_length_4_cov_1_ID_seq2; ACCG >NODE_2_length_4_cov_1_ID_seq2':NODE_2_length_4_cov_1_ID_seq2'; CGGT Fastaq-3.14.0/pyfastaq/tests/data/tasks_test_to_fastg.ids_to_circularise000066400000000000000000000000051276201573500265660ustar00rootroot00000000000000seq2 Fastaq-3.14.0/pyfastaq/tests/data/test_acgtn_only.expected.fa000066400000000000000000000000401276201573500242270ustar00rootroot00000000000000>seq1 acgtACGTnN >seq2 aNcNgNNT Fastaq-3.14.0/pyfastaq/tests/data/test_acgtn_only.in.fa000066400000000000000000000000401276201573500230340ustar00rootroot00000000000000>seq1 acgtACGTnN >seq2 aXcRg.?T Fastaq-3.14.0/pyfastaq/tests/data/utils_test_file_transpose.txt000066400000000000000000000000521276201573500247630ustar00rootroot0000000000000011 12 13 21 22 23 31 32 33 41 42 51 52 53 Fastaq-3.14.0/pyfastaq/tests/data/utils_test_file_transposed.txt000066400000000000000000000000541276201573500251310ustar00rootroot0000000000000011 21 31 41 51 12 22 32 42 52 13 23 33 . 53 Fastaq-3.14.0/pyfastaq/tests/data/utils_test_not_really_zipped.gz000066400000000000000000000000031276201573500252660ustar00rootroot0000000000000042 Fastaq-3.14.0/pyfastaq/tests/data/utils_test_scaffolds.fa000066400000000000000000000000751276201573500234660ustar00rootroot00000000000000>scaf1 ACGT >scaf2 ACNNNGTNA >scaf3 NNAAAANNN >scaf4 NNNNNNN Fastaq-3.14.0/pyfastaq/tests/data/utils_test_scaffolds.fa.to_contigs.fa000066400000000000000000000001111276201573500262110ustar00rootroot00000000000000>scaf1.1.4 ACGT >scaf2.1.2 AC >scaf2.6.7 GT >scaf2.9.9 A >scaf3.3.6 AAAA Fastaq-3.14.0/pyfastaq/tests/data/utils_test_scaffolds.fa.to_contigs.number_contigs.fa000066400000000000000000000000771276201573500312410ustar00rootroot00000000000000>scaf1.1 ACGT >scaf2.1 AC >scaf2.2 GT >scaf2.3 A >scaf3.1 AAAA Fastaq-3.14.0/pyfastaq/tests/data/utils_test_system_call.txt000066400000000000000000000000561276201573500242710ustar00rootroot00000000000000this is the contents of system call test file Fastaq-3.14.0/pyfastaq/tests/intervals_test.py000066400000000000000000000221731276201573500214450ustar00rootroot00000000000000#!/usr/bin/env python3 import unittest from pyfastaq import intervals class TestIntervals(unittest.TestCase): def test_init(self): '''Throw error if try to construct genome_interval from a non-int, or endX'), 'X') with self.assertRaises(sequences.Error): self.assertEqual(sequences.Fasta._get_id_from_header_line(self.fasta, 'X'), 'X') def test_getitem(self): '''getitem() should return the right subsequence''' seq = 'AACGTGTCA' fa = sequences.Fasta('x', seq) self.assertEqual(seq[1], fa[1]) self.assertEqual(seq[0:2], fa[0:2]) self.assertEqual(seq[1:], fa[1:]) def test_len(self): '''len() should return the length of the sequence''' self.assertEqual(5, len(self.fasta)) def test_subseq(self): '''Test subseq''' fa = sequences.Fasta('name', 'ACGTA') self.assertEqual(fa.subseq(1,4), sequences.Fasta('name', 'CGT')) self.assertEqual(fa.subseq(None,4), sequences.Fasta('name', 'ACGT')) self.assertEqual(fa.subseq(1,None), sequences.Fasta('name', 'CGTA')) def test_print_line_length(self): '''__str__ should be formatted correctly with the right number of chars per line of sequence''' line_lengths = [0, 3] correct_files = [os.path.join(data_dir, x) for x in ['sequences_test_one-per-line.fa', 'sequences_test_3-per-line.fa']] for i in range(len(line_lengths)): seq_reader = sequences.file_reader(os.path.join(data_dir, 'sequences_test_one-per-line.fa')) sequences.Fasta.line_length = line_lengths[i] tmp_out = 'tmp.line_length_test.fa' f = utils.open_file_write(tmp_out) for s in seq_reader: print(s, file=f) utils.close(f) self.assertTrue(filecmp.cmp(correct_files[i], tmp_out)) os.unlink(tmp_out) sequences.Fasta.line_length = 60 def test_strip_after_first_whitespace(self): '''Test strip_after_first_whitespace()''' seqs = [ sequences.Fasta('name', 'A'), sequences.Fasta('name foo', 'A'), sequences.Fasta('name foo bar', 'A'), sequences.Fasta('name\tfoo', 'A'), ] for seq in seqs: seq.strip_after_first_whitespace() for seq in seqs: self.assertEqual(seq.id, 'name') def test_strip_illumina_suffix(self): '''Check that /1 and /2 removed correctly from IDs''' seqs = [sequences.Fasta('name/1', 'A'), sequences.Fasta('name/2', 'A'), sequences.Fasta('name', 'A'), sequences.Fasta('name/1/2', 'A'), sequences.Fasta('name/2/1', 'A'), sequences.Fasta('name/3', 'A')] correct_names = ['name', 'name', 'name', 'name/1', 'name/2', 'name/3'] for seq in seqs: seq.strip_illumina_suffix() for i in range(len(seqs)): self.assertEqual(seqs[i].id, correct_names[i]) def test_revcomp(self): '''revcomp() should correctly reverse complement a sequence''' fa = sequences.Fasta('ID', 'ACGTNacgtn') fa.revcomp() self.assertEqual(fa, sequences.Fasta('ID', 'nacgtNACGT')) def test_gaps(self): '''gaps() should find the gaps in a sequence correctly''' test_seqs = [sequences.Fasta('ID', 'ACGT'), sequences.Fasta('ID', 'NACGT'), sequences.Fasta('ID', 'NACGTN'), sequences.Fasta('ID', 'ANNCGT'), sequences.Fasta('ID', 'NANNCGTNN')] correct_gaps = [[], [intervals.Interval(0, 0)], [intervals.Interval(0, 0), intervals.Interval(5, 5)], [intervals.Interval(1, 2)], [intervals.Interval(0, 0), intervals.Interval(2, 3), intervals.Interval(7, 8)]] for i in range(len(test_seqs)): gaps = test_seqs[i].gaps() self.assertListEqual(correct_gaps[i], gaps) def test_contig_coords(self): '''contig_coords() should get the coords of all contigs in a sequence correctly''' test_seqs = [sequences.Fasta('ID', 'ACGT'), sequences.Fasta('ID', 'NACGT'), sequences.Fasta('ID', 'NNACGT'), sequences.Fasta('ID', 'ACGTN'), sequences.Fasta('ID', 'ACGTNN'), sequences.Fasta('ID', 'NANNCGT'), sequences.Fasta('ID', 'ACNNNGTNA'), sequences.Fasta('ID', 'ANNCGTNNAAAAA')] correct_coords = [[intervals.Interval(0,3)], [intervals.Interval(1, 4)], [intervals.Interval(2, 5)], [intervals.Interval(0, 3)], [intervals.Interval(0, 3)], [intervals.Interval(1, 1), intervals.Interval(4,6)], [intervals.Interval(0, 1), intervals.Interval(5, 6), intervals.Interval(8, 8)], [intervals.Interval(0, 0), intervals.Interval(3, 5), intervals.Interval(8, 12)]] for i in range(len(test_seqs)): gaps = test_seqs[i].contig_coords() self.assertListEqual(correct_coords[i], gaps) def test_orfs(self): '''Test orfs()''' test_seqs = [(sequences.Fasta('ID', 'AAACCCGG'), 0, False, [intervals.Interval(0,5)]), (sequences.Fasta('ID', 'AAAACCCGG'), 1, False, [intervals.Interval(1,6)]), (sequences.Fasta('ID', 'AAAAACCCGG'), 2, False, [intervals.Interval(2,7)]), (sequences.Fasta('ID', 'CCGGGTTT'), 0, True, [intervals.Interval(2,7)]), (sequences.Fasta('ID', 'CCGGGTTTT'), 1, True, [intervals.Interval(2,7)]), (sequences.Fasta('ID', 'CCGGGTTTTT'), 2, True, [intervals.Interval(2,7)]), (sequences.Fasta('ID', 'AAACCCTGA'), 0, False, [intervals.Interval(0,8)]), (sequences.Fasta('ID', 'AAACCCTGATAG'), 0, False, [intervals.Interval(0,8)]), (sequences.Fasta('ID', 'AAACCCTGA'), 1, False, [intervals.Interval(1,6)]), (sequences.Fasta('ID', ''), 0, False, []), (sequences.Fasta('ID', 'A'), 0, False, []), (sequences.Fasta('ID', 'AA'), 0, False, []), (sequences.Fasta('ID', 'AAA'), 0, False, [intervals.Interval(0,2)]), (sequences.Fasta('ID', 'AAAAAA'), 0, False, [intervals.Interval(0,5)]), (sequences.Fasta('ID', 'AAA'), 1, False, []), (sequences.Fasta('ID', 'AAA'), 2, False, []), (sequences.Fasta('ID', 'AAA'), 0, True, [intervals.Interval(0,2)]), (sequences.Fasta('ID', 'AAA'), 1, True, []), (sequences.Fasta('ID', 'AAA'), 2, True, []), (sequences.Fasta('ID', 'TAA'), 0, False, []), (sequences.Fasta('ID', 'CTA'), 0, True, [])] for t in test_seqs: orfs = t[0].orfs(frame=t[1], revcomp=t[2]) self.assertListEqual(orfs, t[3]) def test_all_orfs(self): '''Test all_orfs()''' d = {} tasks.file_to_dict(os.path.join(data_dir, 'sequences_test_orfs.fa'), d) seq = d['1'] orfs = seq.all_orfs(min_length=120) expected = [ (intervals.Interval(27, 221), False), (intervals.Interval(44, 226), False), (intervals.Interval(48, 170), True), (intervals.Interval(109, 240), False), (intervals.Interval(143, 265), True), (intervals.Interval(227, 421), False), (intervals.Interval(277, 432), True), (intervals.Interval(286, 477), False), (intervals.Interval(288, 518), True), (intervals.Interval(562, 702), False), (intervals.Interval(600, 758), False), (intervals.Interval(605, 817), False), (intervals.Interval(818, 937), False), (intervals.Interval(835, 987), False), (intervals.Interval(864, 998), False) ] self.assertEqual(len(orfs), len(expected)) for i in range(len(orfs)): print(orfs[i][0], expected[i][0]) self.assertEqual(orfs[i][0], expected[i][0]) self.assertEqual(orfs[i][1], expected[i][1]) def test_is_complete_orf(self): '''Test is_complete_orf''' tests = [ (sequences.Fasta('ID', 'TTT'), False), (sequences.Fasta('ID', 'TTTTAA'), True), (sequences.Fasta('ID', 'TTTTAATAA'), False), (sequences.Fasta('ID', 'TTGTAA'), True), (sequences.Fasta('ID', 'TTTAAC'), True), (sequences.Fasta('ID', 'TGA'), False), (sequences.Fasta('ID', 'TGAA'), False), ] for t in tests: self.assertEqual(t[0].is_complete_orf(), t[1]) def test_looks_like_gene(self): '''Test looks_like_gene''' tests = [ (sequences.Fasta('ID', 'TTT'), False), (sequences.Fasta('ID', 'TTGTAA'), True), (sequences.Fasta('ID', 'ttgTAA'), True), (sequences.Fasta('ID', 'TTGTTTTAA'), True), (sequences.Fasta('ID', 'TTGTAATTTTAA'), False), (sequences.Fasta('ID', 'TTGTTTTGAA'), False), ] for t in tests: self.assertEqual(t[0].looks_like_gene(), t[1]) sequences.genetic_code = 1 self.assertFalse(sequences.Fasta('ID', 'ATTCAGTAA').looks_like_gene()) sequences.genetic_code = 11 self.assertTrue(sequences.Fasta('ID', 'ATTCAGTAA').looks_like_gene()) sequences.genetic_code = 1 def test_make_into_gene_fasta(self): '''Test make_into_gene fasta''' print('sequences.genetic_code', sequences.genetic_code) tests = [ (sequences.Fasta('ID', 'T'), None), (sequences.Fasta('ID', 'TT'), None), (sequences.Fasta('ID', 'TTT'), None), (sequences.Fasta('ID', 'TTG'), None), (sequences.Fasta('ID', 'TAA'), None), (sequences.Fasta('ID', 'TTGAAATAA'), (sequences.Fasta('ID', 'TTGAAATAA'), '+', 0)), (sequences.Fasta('ID', 'TTGAAATAT'), None), (sequences.Fasta('ID', 'TTGTAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 0)), (sequences.Fasta('ID', 'TTGTAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 0)), (sequences.Fasta('ID', 'TTGTAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 0)), (sequences.Fasta('ID', 'TTGTAAAAA'), None), (sequences.Fasta('ID', 'ATTGTAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 1)), (sequences.Fasta('ID', 'ATTGTAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 1)), (sequences.Fasta('ID', 'ATTGTAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 1)), (sequences.Fasta('ID', 'ATTGTAAAAA'), None), (sequences.Fasta('ID', 'AATTGTAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 2)), (sequences.Fasta('ID', 'AATTGTAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 2)), (sequences.Fasta('ID', 'AATTGTAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 2)), (sequences.Fasta('ID', 'AATTGTAAAAA'), None), (sequences.Fasta('ID', 'TTACAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 0)), (sequences.Fasta('ID', 'ATTACAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 0)), (sequences.Fasta('ID', 'AATTACAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 0)), (sequences.Fasta('ID', 'AAATTACAA'), None), (sequences.Fasta('ID', 'TTACAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 1)), (sequences.Fasta('ID', 'ATTACAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 1)), (sequences.Fasta('ID', 'AATTACAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 1)), (sequences.Fasta('ID', 'AAATTACAAA'), None), (sequences.Fasta('ID', 'TTACAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 2)), (sequences.Fasta('ID', 'ATTACAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 2)), (sequences.Fasta('ID', 'AATTACAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 2)), (sequences.Fasta('ID', 'AAATTACAAAA'), None), ] for seq, expected in tests: self.assertEqual(seq.make_into_gene(), expected) def test_make_into_gene_fastq(self): '''Test make_into_gene fastq''' print('sequences.genetic_code', sequences.genetic_code) tests = [ (sequences.Fastq('ID', 'T', '1'), None), (sequences.Fastq('ID', 'TT', '12'), None), (sequences.Fastq('ID', 'TTT', '123'), None), (sequences.Fastq('ID', 'TTG', '123'), None), (sequences.Fastq('ID', 'TAA', '123'), None), (sequences.Fastq('ID', 'TTGAAATAA', '123456789'), (sequences.Fastq('ID', 'TTGAAATAA', '123456789'), '+', 0)), (sequences.Fastq('ID', 'TTGAAATAT', '123456789'), None), (sequences.Fastq('ID', 'TTGTAA', '123456'), (sequences.Fastq('ID', 'TTGTAA', '123456'), '+', 0)), (sequences.Fastq('ID', 'TTGTAAA', '1234567'), (sequences.Fastq('ID', 'TTGTAA', '123456'), '+', 0)), (sequences.Fastq('ID', 'TTGTAAAA', '12345678'), (sequences.Fastq('ID', 'TTGTAA', '123456'), '+', 0)), (sequences.Fastq('ID', 'TTGTAAAAA', '123456789'), None), (sequences.Fastq('ID', 'ATTGTAA', '1234567'), (sequences.Fastq('ID', 'TTGTAA', '234567'), '+', 1)), (sequences.Fastq('ID', 'ATTGTAAA', '12345678'), (sequences.Fastq('ID', 'TTGTAA', '234567'), '+', 1)), (sequences.Fastq('ID', 'ATTGTAAAA', '123456789'), (sequences.Fastq('ID', 'TTGTAA', '234567'), '+', 1)), (sequences.Fastq('ID', 'ATTGTAAAAA', '123456789A'), None), (sequences.Fastq('ID', 'AATTGTAA', '12345678'), (sequences.Fastq('ID', 'TTGTAA', '345678'), '+', 2)), (sequences.Fastq('ID', 'AATTGTAAA', '123456789'), (sequences.Fastq('ID', 'TTGTAA', '345678'), '+', 2)), (sequences.Fastq('ID', 'AATTGTAAAA', '123456789A'), (sequences.Fastq('ID', 'TTGTAA', '345678'), '+', 2)), (sequences.Fastq('ID', 'AATTGTAAAAA', '123456789AB'), None), (sequences.Fastq('ID', 'TTACAA', '123456'), (sequences.Fastq('ID', 'TTGTAA', '654321'), '-', 0)), (sequences.Fastq('ID', 'ATTACAA', '1234567'), (sequences.Fastq('ID', 'TTGTAA', '765432'), '-', 0)), (sequences.Fastq('ID', 'AATTACAA', '12345678'), (sequences.Fastq('ID', 'TTGTAA', '876543'), '-', 0)), (sequences.Fastq('ID', 'AAATTACAA', '123456789'), None), (sequences.Fastq('ID', 'TTACAAA', '1234567'), (sequences.Fastq('ID', 'TTGTAA', '654321'), '-', 1)), (sequences.Fastq('ID', 'ATTACAAA', '12345678'), (sequences.Fastq('ID', 'TTGTAA', '765432'), '-', 1)), (sequences.Fastq('ID', 'AATTACAAA', '123456789'), (sequences.Fastq('ID', 'TTGTAA', '876543'), '-', 1)), (sequences.Fastq('ID', 'AAATTACAAA', '123456789A'), None), (sequences.Fastq('ID', 'TTACAAAA', '12345678'), (sequences.Fastq('ID', 'TTGTAA', '654321'), '-', 2)), (sequences.Fastq('ID', 'ATTACAAAA', '123456789'), (sequences.Fastq('ID', 'TTGTAA', '765432'), '-', 2)), (sequences.Fastq('ID', 'AATTACAAAA', '123456789A'), (sequences.Fastq('ID', 'TTGTAA', '876543'), '-', 2)), (sequences.Fastq('ID', 'AAATTACAAAA', '123456789AB'), None), ] for seq, expected in tests: self.assertEqual(seq.make_into_gene(), expected) def test_is_all_Ns(self): '''Test is_all_Ns()''' self.assertTrue(sequences.Fasta('ID', 'n').is_all_Ns()) self.assertTrue(sequences.Fasta('ID', 'N').is_all_Ns()) self.assertTrue(sequences.Fasta('ID', 'nNn').is_all_Ns()) self.assertFalse(sequences.Fasta('ID', 'a').is_all_Ns()) self.assertFalse(sequences.Fasta('ID', '').is_all_Ns()) self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns()) self.assertFalse(sequences.Fasta('ID', 'naN').is_all_Ns()) self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns(start=0, end=0)) self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns(start=0, end=1)) self.assertTrue(sequences.Fasta('ID', 'anNg').is_all_Ns(start=1, end=1)) self.assertTrue(sequences.Fasta('ID', 'anNg').is_all_Ns(start=1, end=2)) self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns(start=1)) self.assertTrue(sequences.Fasta('ID', 'anN').is_all_Ns(start=1)) self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns(end=1)) self.assertTrue(sequences.Fasta('ID', 'nNA').is_all_Ns(end=1)) with self.assertRaises(sequences.Error): sequences.Fasta('ID', 'anNg').is_all_Ns(start=1, end=0) def test_trim_Ns(self): '''trim_Ns() should do the right trimming of a sequence''' fa = sequences.Fasta('ID', 'ANNANA') test_seqs = [sequences.Fasta('ID', 'ANNANA'), sequences.Fasta('ID', 'NANNANA'), sequences.Fasta('ID', 'NANNANAN'), sequences.Fasta('ID', 'ANNANAN'), sequences.Fasta('ID', 'NNNNNNANNANAN'), sequences.Fasta('ID', 'NNANNANANn')] for s in test_seqs: s.trim_Ns() self.assertEqual(fa, s) def test_add_insertions(self): '''Test add_insertions''' fa = sequences.Fasta('X', 'acgtacgtacgt') fa.add_insertions(skip=4, window=0, test=True) self.assertEqual(fa, sequences.Fasta('X', 'acgtNacgtNacgt')) def test_replace_bases(self): '''Check that bases get replaced correctly''' fa = sequences.Fasta('X', 'AUCGTUUACT') fa.replace_bases('U', 'T') self.assertEqual(fa, sequences.Fasta('X', 'ATCGTTTACT')) def test_replace_non_acgt(self): '''test replace_non_acgt''' tests = [ ('acgtACGTnN', 'acgtACGTnN'), ('abc.g-T?aRC1T', 'aNcNgNTNaNCNT') ] for seq, expected in tests: fa = sequences.Fasta('id', seq) fa.replace_non_acgt() self.assertEqual(expected, fa.seq) def test_replace_interval(self): '''Test replace_interval()''' fa = sequences.Fasta('ID', 'ACGTA') fa.replace_interval(0, 0, 'NEW') self.assertEqual(fa, sequences.Fasta('ID', 'NEWCGTA')) fa = sequences.Fasta('ID', 'ACGTA') fa.replace_interval(4, 4, 'NEW') self.assertEqual(fa, sequences.Fasta('ID', 'ACGTNEW')) fa = sequences.Fasta('ID', 'ACGTA') fa.replace_interval(2, 3, 'NEW') self.assertEqual(fa, sequences.Fasta('ID', 'ACNEWA')) fa = sequences.Fasta('ID', 'ACGTA') with self.assertRaises(sequences.Error): fa.replace_interval(3,2,'x') with self.assertRaises(sequences.Error): fa.replace_interval(1,5,'x') with self.assertRaises(sequences.Error): fa.replace_interval(5,10,'x') fq = sequences.Fastq('ID', 'ACGTA', 'ABCDE') fq.replace_interval(0, 0, 'NEW', 'III') self.assertEqual(fq, sequences.Fastq('ID', 'NEWCGTA', 'IIIBCDE')) fq = sequences.Fastq('ID', 'ACGTA', 'ABCDE') fq.replace_interval(4, 4, 'NEW', 'III') self.assertEqual(fq, sequences.Fastq('ID', 'ACGTNEW', 'ABCDIII')) fq = sequences.Fastq('ID', 'ACGTA', 'ABCDE') fq.replace_interval(2, 3, 'NEW', 'III') self.assertEqual(fq, sequences.Fastq('ID', 'ACNEWA', 'ABIIIE')) with self.assertRaises(sequences.Error): fq.replace_interval(1,1,'x', 'xx') def test_search_string(self): '''Check that search_string() finds all the hits''' fa = sequences.Fasta('X', 'AAA') hits = fa.search('G') self.assertTrue(len(hits) == 0) hits = fa.search('AAA') self.assertListEqual(hits, [(0, '+')]) hits = fa.search('AA') self.assertListEqual(hits, [(0, '+'), (1, '+')]) hits = fa.search('TTT') self.assertListEqual(hits, [(0, '-')]) def test_to_Fastq(self): '''Check to_Fastq converts OK, including out of range quality scores''' fa = sequences.Fasta('X', 'AAAAA') quals = [-1, 0, 40, 93, 94] self.assertEqual(sequences.Fastq('X', 'AAAAA', '!!I~~'), fa.to_Fastq(quals)) with self.assertRaises(sequences.Error): fa.to_Fastq('AAAAAAAAAAAAA') def test_translate(self): '''Test nucleotide -> amino acid conversion works on Fasta''' fa = sequences.Fasta('ID', 'GCAGCCGCGGCTAGAAGGCGACGCCGGCGTAACAATGACGATTGCTGTGAAGAGCAACAGGGAGGCGGGGGTCACCATATAATCATTTTATTGCTACTCCTGCTTAAAAAGATGTTCTTTCCACCCCCGCCTAGCAGTTCATCCTCGTCTACAACCACGACTTGGTACTATGTAGTCGTGGTTTAATAGTGA') self.assertEqual(sequences.Fasta('ID', 'AAAARRRRRRNNDDCCEEQQGGGGHHIIILLLLLLKKMFFPPPPSSSSSSTTTTWYYVVVV***'), fa.translate()) self.assertEqual(sequences.Fasta('ID', 'QPRLEGDAGVTMTIAVKSNREAGVTI*SFYCYSCLKRCSFHPRLAVHPRLQPRLGTM*SWFNS'), fa.translate(frame=1)) print(fa.translate(frame=1)) self.assertEqual(sequences.Fasta('ID', 'SRG*KATPA*Q*RLL*RATGRRGSPYNHFIATPA*KDVLSTPA*QFILVYNHDLVLCSRGLIV'), fa.translate(frame=2)) def test_expand_nucleotides(self): '''Test expand_nucleotides''' tests = [ (sequences.Fasta('1', 'A'), [sequences.Fasta('1.1', 'A')]), (sequences.Fasta('2', 'C'), [sequences.Fasta('2.1', 'C')]), (sequences.Fasta('3', 'G'), [sequences.Fasta('3.1', 'G')]), (sequences.Fasta('4', 'T'), [sequences.Fasta('4.1', 'T')]), (sequences.Fasta('6', 'R'), [sequences.Fasta('6.1', 'A'), sequences.Fasta('6.2', 'G')]), (sequences.Fasta('7', 'Y'), [sequences.Fasta('7.1', 'C'), sequences.Fasta('7.2', 'T')]), (sequences.Fasta('8', 'S'), [sequences.Fasta('8.1', 'C'), sequences.Fasta('8.2', 'G')]), (sequences.Fasta('9', 'W'), [sequences.Fasta('9.1', 'A'), sequences.Fasta('9.2', 'T')]), (sequences.Fasta('10', 'K'), [sequences.Fasta('10.1', 'G'), sequences.Fasta('10.2', 'T')]), (sequences.Fasta('11', 'M'), [sequences.Fasta('11.1', 'A'), sequences.Fasta('11.2', 'C')]), (sequences.Fasta('12', 'B'), [sequences.Fasta('12.1', 'C'), sequences.Fasta('12.2', 'G'), sequences.Fasta('12.3', 'T')]), (sequences.Fasta('13', 'D'), [sequences.Fasta('13.1', 'A'), sequences.Fasta('13.2', 'G'), sequences.Fasta('13.3', 'T')]), (sequences.Fasta('14', 'H'), [sequences.Fasta('14.1', 'A'), sequences.Fasta('14.2', 'C'), sequences.Fasta('14.3', 'T')]), (sequences.Fasta('15', 'V'), [sequences.Fasta('15.1', 'A'), sequences.Fasta('15.2', 'C'), sequences.Fasta('15.3', 'G')]), (sequences.Fasta('16', 'N'), [sequences.Fasta('16.1', 'A'), sequences.Fasta('16.2', 'C'), sequences.Fasta('16.3', 'G'), sequences.Fasta('16.4', 'T')]), (sequences.Fasta('17', 'ART'), [sequences.Fasta('17.1', 'AAT'), sequences.Fasta('17.2', 'AGT')]), (sequences.Fasta('18', 'ARRT'), [sequences.Fasta('18.1', 'AAAT'), sequences.Fasta('18.2', 'AAGT'), sequences.Fasta('18.3', 'AGAT'), sequences.Fasta('18.4', 'AGGT')]), (sequences.Fasta('19', 'ARTR'), [sequences.Fasta('19.1', 'AATA'), sequences.Fasta('19.2', 'AATG'), sequences.Fasta('19.3', 'AGTA'), sequences.Fasta('19.4', 'AGTG')]), (sequences.Fastq('20', 'ART', 'GHI'), [sequences.Fastq('20.1', 'AAT', 'GHI'), sequences.Fastq('20.2', 'AGT', 'GHI')]), ] for t in tests: self.assertListEqual(t[0].expand_nucleotides(), t[1]) def test_split_capillary_id(self): '''Tests that we get information from a sanger capillary read name OK''' ids = ['abcde.p1k', 'abcde.x.p1k', 'abcde.p1ka', 'abcde.q1k', 'abcde.w2k'] expected = [{'prefix': 'abcde', 'dir': 'fwd', 'suffix': 'p1k'}, {'prefix': 'abcde.x', 'dir': 'fwd', 'suffix': 'p1k'}, {'prefix': 'abcde', 'dir': 'fwd', 'suffix': 'p1ka'}, {'prefix': 'abcde', 'dir': 'rev', 'suffix': 'q1k'}, {'prefix': 'abcde', 'dir': 'unk', 'suffix': 'w2k'}] for i in range(len(ids)): fa = sequences.Fasta(ids[i], 'A') self.assertEqual(fa.split_capillary_id(), expected[i]) with self.assertRaises(sequences.Error): fa = sequences.Fasta('name', 'A') fa.split_capillary_id() class TestEmbl(unittest.TestCase): def test_get_id_from_header_line(self): '''Test get id from header line of EMBL''' embl = sequences.Embl('ID', 'ACGT') self.assertEqual(embl._get_id_from_header_line('ID X; blah'), 'X') self.assertEqual(embl._get_id_from_header_line('LOCUS X foo'), 'X') with self.assertRaises(sequences.Error): self.assertEqual(embl._get_id_from_header_line('ID X;'), 'X') with self.assertRaises(sequences.Error): self.assertEqual(embl._get_id_from_header_line('XX X;'), 'X') def test_get_next_from_embl_file(self): f_in = utils.open_file_read(os.path.join(data_dir, 'sequences_test.embl')) embl = sequences.Embl() counter = 1 while embl.get_next_from_file(f_in): self.assertEqual(embl, sequences.Fasta('seq' + str(counter), expected_embl[counter-1])) counter += 1 utils.close(f_in) def test_get_next_from_gbk_file(self): f_in = utils.open_file_read(os.path.join(data_dir, 'sequences_test.gbk')) embl = sequences.Embl() counter = 1 expected = [ 'gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaatgccatgactcagattctaattttaagctattcaatttctctttgatc', 'gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaatgccatgactcagattctaattttaagctattcaatttctctttgaaa'] while embl.get_next_from_file(f_in): self.assertEqual(embl, sequences.Fasta('NAME' + str(counter), expected[counter-1])) counter += 1 utils.close(f_in) class TestFastq(unittest.TestCase): def setUp(self): self.fastq = sequences.Fastq('ID', 'ACGTA', 'IIIII') def test_init(self): '''__init__ should get the ID, sequence and quality correctly''' self.assertEqual(self.fastq.id, 'ID') self.assertEqual(self.fastq.seq, 'ACGTA') self.assertEqual(self.fastq.qual, 'IIIII') def test_init_length_mismatch(self): '''__init__ should raise an error when length of seq and quality not the same''' with self.assertRaises(sequences.Error): sequences.Fastq('X', 'A', 'II') def test_get_next_from_file(self): '''get_next_from_file() should read seqs from OK, and raise error at badly formatted file''' bad_files = ['sequences_test_fail_no_AT.fq', 'sequences_test_fail_no_seq.fq', 'sequences_test_fail_no_plus.fq', 'sequences_test_fail_no_qual.fq'] bad_files = [os.path.join(data_dir, x) for x in bad_files] for fname in bad_files: f_in = utils.open_file_read(fname) fq = sequences.Fastq() with self.assertRaises(sequences.Error): while fq.get_next_from_file(f_in): pass utils.close(f_in) fname = os.path.join(data_dir, 'sequences_test_good_file.fq') try: f_in = open(fname) except IOError: print("Error opening '" + fname + "'", file=sys.stderr) sys.exit(1) fq = sequences.Fastq() while fq.get_next_from_file(f_in): self.assertEqual(fq, sequences.Fastq('ID', 'ACGTA', 'IIIII')) utils.close(f_in) def test_subseq(self): '''Test subseq''' fq = sequences.Fastq('name', 'ACGTA', 'FGHIJ') self.assertEqual(fq.subseq(1,4), sequences.Fastq('name', 'CGT', 'GHI')) self.assertEqual(fq.subseq(None,4), sequences.Fastq('name', 'ACGT', 'FGHI')) self.assertEqual(fq.subseq(1,None), sequences.Fastq('name', 'CGTA', 'GHIJ')) def test_revcomp(self): '''revcomp() should correctly reverse complement a sequence''' fq = sequences.Fastq('ID', 'ACGTNacgtn', '1234567890') fq.revcomp() self.assertEqual(fq, sequences.Fastq('ID', 'nacgtNACGT', '0987654321')) def test_trim_Ns(self): '''trim_Ns() should do the right trimming of a fastq sequence''' fq = sequences.Fastq('ID', 'ANNANA', '111111') test_seqs = [sequences.Fastq('ID', 'ANNANA', '111111'), sequences.Fastq('ID', 'NANNANA', '1111111'), sequences.Fastq('ID', 'NANNANAN', '11111111'), sequences.Fastq('ID', 'ANNANAN', '1111111'), sequences.Fastq('ID', 'NNNNNNANNANAN', '1111111111111'), sequences.Fastq('ID', 'NNANNANANn', '1111111111')] for s in test_seqs: s.trim_Ns() self.assertEqual(fq, s) def test_trim(self): '''trim() should trim the right number of bases off start and end''' fq = sequences.Fastq('ID', '1234567890', '1234567890') fq.trim(0, 0) self.assertEqual(fq, sequences.Fastq('ID', '1234567890', '1234567890')) fq = sequences.Fastq('ID', '1234567890', '1234567890') fq.trim(1, 0) self.assertEqual(fq, sequences.Fastq('ID', '234567890', '234567890')) fq = sequences.Fastq('ID', '1234567890', '1234567890') fq.trim(0, 1) self.assertEqual(fq, sequences.Fastq('ID', '123456789', '123456789')) fq = sequences.Fastq('ID', '1234567890', '1234567890') fq.trim(2, 2) self.assertEqual(fq, sequences.Fastq('ID', '345678', '345678')) def test_to_Fasta_and_qual(self): '''Check to_Fasta_and_qual converts quality scores correctly''' fq = sequences.Fastq('ID', 'ACGT', '>ADI') (fa, qual) = fq.to_Fasta_and_qual() self.assertEqual(fa, sequences.Fasta('ID', 'ACGT')) self.assertListEqual(qual, [29, 32, 35, 40]) def test_translate(self): '''Test nucleatide -> amino acid conversion works on Fasta''' fq = sequences.Fastq('ID', 'GCAGCCGCGGCTAGAAGGCGACGCCGGCGTAACAATGACGATTGCTGTGAAGAGCAACAGGGAGGCGGGGGTCACCATATAATCATTTTATTGCTACTCCTGCTTAAAAAGATGTTCTTTCCACCCCCGCCTAGCAGTTCATCCTCGTCTACAACCACGACTTGGTACTATGTAGTCGTGGTTTAATAGTGA', 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII') self.assertEqual(sequences.Fastq('ID', 'AAAARRRRRRNNDDCCEEQQGGGGHHIIILLLLLLKKMFFPPPPSSSSSSTTTTWYYVVVV***', 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII'), fq.translate()) class TestFileReader(unittest.TestCase): def test_file_reader_fasta(self): '''file_reader should iterate through a fasta file correctly''' reader = sequences.file_reader(os.path.join(data_dir, 'sequences_test.fa')) counter = 1 for seq in reader: self.assertEqual(seq, sequences.Fasta(str(counter), 'ACGTA')) counter += 1 def test_file_reader_fastq(self): '''file_reader should iterate through a fastq file correctly''' reader = sequences.file_reader(os.path.join(data_dir, 'sequences_test_good_file.fq')) for seq in reader: self.assertEqual(seq, sequences.Fastq('ID', 'ACGTA', 'IIIII')) def test_file_reader_bad_format(self): '''file_reader should die properly when not given fasta or fastq file''' with self.assertRaises(sequences.Error): reader = sequences.file_reader(os.path.join(data_dir, 'sequences_test_not_a_fastaq_file')) for seq in reader: pass def test_file_reader_gff(self): '''Test read gff file''' good_files = [ 'sequences_test_gffv3.gff', 'sequences_test_gffv3.no_FASTA_line.gff' ] good_files = [os.path.join(data_dir, x) for x in good_files] for f in good_files: reader = sequences.file_reader(f) counter = 1 for seq in reader: self.assertEqual(seq, sequences.Fasta('seq' + str(counter), 'ACGTACGTAC')) counter += 1 bad_files = [ 'sequences_test_gffv3.no_seq.gff', 'sequences_test_gffv3.no_seq.2.gff' ] bad_files = [os.path.join(data_dir, x) for x in bad_files] for filename in bad_files: with self.assertRaises(sequences.Error): reader = sequences.file_reader(filename) for seq in reader: pass def test_file_reader_embl(self): '''Test read embl file''' reader = sequences.file_reader(os.path.join(data_dir, 'sequences_test.embl')) counter = 1 for seq in reader: self.assertEqual(seq, sequences.Fasta('seq' + str(counter), expected_embl[counter-1])) counter += 1 bad_files = [ 'sequences_test.embl.bad', 'sequences_test.embl.bad2', ] bad_files = [os.path.join(data_dir, x) for x in bad_files] for filename in bad_files: with self.assertRaises(sequences.Error): reader = sequences.file_reader(filename) for seq in reader: pass def test_file_reader_phylip(self): '''Test read phylip file''' test_files = [ 'sequences_test_phylip.interleaved', 'sequences_test_phylip.interleaved2', 'sequences_test_phylip.sequential' ] test_files = [os.path.join(data_dir, f) for f in test_files] expected_seqs = [ sequences.Fasta('Turkey', 'AACTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT'), sequences.Fasta('Salmo_gair', 'AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT'), sequences.Fasta('H. Sapiens', 'ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA') ] for fname in test_files: reader = sequences.file_reader(fname) i = 0 for seq in reader: self.assertEqual(expected_seqs[i], seq) i += 1 # files made by seaview are a little different in the first line. # Test one of these expected_seqs = [ sequences.Fasta('seq1', 96 * 'G' + 'T'), sequences.Fasta('seq2', 94 * 'A' + 'G') ] reader = sequences.file_reader(os.path.join(data_dir, 'sequences_test_phylip.made_by_seaview')) i = 0 for seq in reader: print(seq) self.assertEqual(expected_seqs[i], seq) i += 1 class TestOther(unittest.TestCase): def test_orfs_from_aa_seq(self): '''Test _orfs_from_aa_seq()''' test_seqs = ['', '*', '**', 'A', 'A*A*A', 'AB**CDE*AB', '*ABCDE*', '**ABCDE**'] correct_coords = [[], [], [], [intervals.Interval(0, 0)], [intervals.Interval(0, 1), intervals.Interval(2, 3),intervals.Interval(4, 4)], [intervals.Interval(0, 2), intervals.Interval(4, 7), intervals.Interval(8, 9)], [intervals.Interval(1, 6)], [intervals.Interval(2, 7)]] for i in range(len(test_seqs)): orfs = sequences._orfs_from_aa_seq(test_seqs[i]) self.assertListEqual(correct_coords[i], orfs) if __name__ == '__main__': unittest.main() Fastaq-3.14.0/pyfastaq/tests/tasks_test.py000066400000000000000000001030361276201573500205610ustar00rootroot00000000000000#!/usr/bin/env python3 import sys import filecmp import os import unittest from pyfastaq import tasks, sequences modules_dir = os.path.dirname(os.path.abspath(sequences.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class Error (Exception): pass class TestACGTN_only(unittest.TestCase): def test_acgtn_only(self): '''Test acgtn_only''' tmpfile = 'tmp.test_acgtn_only.fa' infile = os.path.join(data_dir, 'test_acgtn_only.in.fa') expected = os.path.join(data_dir, 'test_acgtn_only.expected.fa') tasks.acgtn_only(infile, tmpfile) self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) os.unlink(tmpfile) class TestCafToFastq(unittest.TestCase): def test_caf_to_fastq_default(self): '''Test caf_to_fastq with no filtering''' tmpfile = 'tmp.fq' tasks.caf_to_fastq(os.path.join(data_dir, 'caf_test.caf'), tmpfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'caf_test.to_fastq.no_trim.min_length_0.fq'), tmpfile, shallow=False)) os.unlink(tmpfile) def test_caf_to_fastq_trim_and_min_length(self): '''Test caf_to_fastq with trimming and min_length''' tmpfile = 'tmp.fq' tasks.caf_to_fastq(os.path.join(data_dir, 'caf_test.caf'), tmpfile, trim=True, min_length=6) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'caf_test.to_fastq.trim.min_length_6.fq'), tmpfile, shallow=False)) os.unlink(tmpfile) class TestCapillaryToPairs(unittest.TestCase): def test_capillary_to_pairs(self): '''Check that capillary reads file converted to paired and unpaired''' tmp_prefix = 'tmp.cap_to_pairs' tasks.capillary_to_pairs(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa'), tmp_prefix) # sequences have been hashed, so could be in any order in # output files. So need to check contents of files are OK d_correct_paired = {} d_correct_unpaired = {} tasks.file_to_dict(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa.paired.gz'), d_correct_paired) tasks.file_to_dict(os.path.join(data_dir, 'sequences_test_cap_to_read_pairs.fa.unpaired.gz'), d_correct_unpaired) d_test_paired = {} d_test_unpaired = {} tasks.file_to_dict(tmp_prefix + '.paired.gz', d_test_paired) tasks.file_to_dict(tmp_prefix + '.unpaired.gz', d_test_unpaired) self.assertDictEqual(d_test_paired, d_correct_paired) self.assertDictEqual(d_test_unpaired, d_correct_unpaired) os.unlink(tmp_prefix + '.paired.gz') os.unlink(tmp_prefix + '.unpaired.gz') class TestDeinterleave(unittest.TestCase): def test_deinterleave(self): '''deinterleave should deal with an interleaved file correctly''' tmp_1 = 'tmp.deinterleaved_1.fa' tmp_2 = 'tmp.deinterleaved_2.fa' tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved.fa'), tmp_1, tmp_2) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_1.fa'), tmp_1)) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_2.fa'), tmp_2)) tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved.fq'), tmp_1, tmp_2, fasta_out=True) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_1.fa'), tmp_1)) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_deinterleaved_2.fa'), tmp_2)) with self.assertRaises(tasks.Error): tasks.deinterleave(os.path.join(data_dir, 'sequences_test_interleaved_bad.fa'), tmp_1, tmp_2) os.unlink(tmp_1) os.unlink(tmp_2) class TestEnumerateNames(unittest.TestCase): def test_enumerate_names(self): '''Test enomereate_names works with all options''' outfile = 'tmp.enumerate_seqs.fa' rename_out = outfile + '.rename' tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.1'), outfile)) tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile, rename_file=rename_out) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.1'), outfile)) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.1.rename_file'), rename_out)) tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile, start_index=2) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.start.2'), outfile)) tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile, keep_illumina_suffix=True) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.keep_suffix'), outfile)) tasks.enumerate_names(os.path.join(data_dir, 'sequences_test_enumerate_names.fa'), outfile, suffix='.SUFFIX') self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_enumerate_names.fa.out.add_suffix'), outfile, shallow=False)) os.unlink(outfile) os.unlink(rename_out) class TestExpandNucleotides(unittest.TestCase): def test_expand_nucleoties(self): '''Test expand_nucleotides''' tmp = 'tmp.expanded' fq_in = os.path.join(data_dir, 'tasks_test_expend_nucleotides.in.fq') fa_in = os.path.join(data_dir, 'tasks_test_expend_nucleotides.in.fa') fq_expected = os.path.join(data_dir, 'tasks_test_expend_nucleotides.out.fq') fa_expected = os.path.join(data_dir, 'tasks_test_expend_nucleotides.out.fa') tasks.expand_nucleotides(fq_in, tmp) self.assertTrue(filecmp.cmp(fq_expected, tmp, shallow=False)) os.unlink(tmp) tasks.expand_nucleotides(fa_in, tmp) self.assertTrue(filecmp.cmp(fa_expected, tmp, shallow=False)) os.unlink(tmp) class TestExtendGaps(unittest.TestCase): def test_trim_contigs(self): '''Test that gap extension works''' outfile = 'tmp.gap_extend.fa' tasks.trim_contigs(os.path.join(data_dir, 'sequences_test_trim_contigs.fa'), outfile, trim=2) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_trim_contigs.fa.out'), outfile)) os.unlink(outfile) class TestFastqToMiraXml(unittest.TestCase): def test_fastaq_to_mira_xml(self): '''check that fastaq_to_mira_xml makes the correct xml file from a fastq file''' tmp = 'tmp.mira.xml' tasks.fastaq_to_mira_xml(os.path.join(data_dir, 'sequences_test_good_file.fq'), tmp) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_good_file_mira.xml'), tmp)) os.unlink(tmp) class TestFastaqToOrfsGFF(unittest.TestCase): def test_fastaq_to_orfs_gff(self): '''Test fastaq_to_orfs_gff''' outfile = 'tmp.orfs.gff' tasks.fastaq_to_orfs_gff(os.path.join(data_dir, 'sequences_test_orfs.fa'), outfile, min_length=120) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_orfs.gff'), outfile, shallow=False)) os.unlink(outfile) class TestFilter(unittest.TestCase): def test_length_filter(self): '''Check that filtering by length works as expected''' infile = os.path.join(data_dir, 'sequences_test_length_filter.fa') correct_files = [os.path.join(data_dir, 'sequences_test_length_filter.min-0.max-1.fa'), os.path.join(data_dir, 'sequences_test_length_filter.min-0.max-inf.fa'), os.path.join(data_dir, 'sequences_test_length_filter.min-4.max-4.fa')] cutoffs = [(0, 1), (0, float('inf')), (4, 4)] for i in range(len(cutoffs)): outfile = 'tmp.length_filter.fa' tasks.filter(infile, outfile, minlength=cutoffs[i][0], maxlength=cutoffs[i][1]) self.assertTrue(filecmp.cmp(correct_files[i], outfile)) os.unlink(outfile) def test_regex_filter(self): '''Check that filtering by name regex works as expected''' infile = os.path.join(data_dir, 'sequences_test_filter_by_regex.fa') correct_files = [os.path.join(data_dir, 'sequences_test_filter_by_regex.numeric.fa'), os.path.join(data_dir, 'sequences_test_filter_by_regex.first-of-pair.fa'), os.path.join(data_dir, 'sequences_test_filter_by_regex.first-char-a.fa')] regexes = ['^[0-9]+$', '/1$', '^a'] for i in range(len(regexes)): outfile = 'tmp.regex_filter.fa' tasks.filter(infile, outfile, regex=regexes[i]) self.assertTrue(filecmp.cmp(correct_files[i], outfile)) os.unlink(outfile) def test_ids_from_file_filter(self): '''Test that can extract reads from a file of read names''' infile = os.path.join(data_dir, 'sequences_test_filter_by_ids_file.fa') outfile = 'tmp.ids_file_filter.fa' tasks.filter(infile, outfile, ids_file=infile + '.ids') self.assertTrue(filecmp.cmp(infile + '.filtered', outfile)) os.unlink(outfile) def test_invert_filter(self): '''Test that inverting filtering works''' infile = os.path.join(data_dir, 'sequences_test_filter_by_ids_file.fa') outfile = 'tmp.ids_file_filter.fa' tasks.filter(infile, outfile, ids_file=infile + '.ids', invert=True) self.assertTrue(filecmp.cmp(infile + '.filtered.invert', outfile)) os.unlink(outfile) def test_paired_both_pass(self): '''Test filter with paired file both pass''' infile1 = os.path.join(data_dir, 'tasks_test_filter_paired_both_pass.in_1.fa') infile2 = os.path.join(data_dir, 'tasks_test_filter_paired_both_pass.in_2.fa') outfile1 = 'tmp.filter_both_pass_1.fa' outfile2 = 'tmp.filter_both_pass_2.fa' expected1 = os.path.join(data_dir, 'tasks_test_filter_paired_both_pass.out_1.fa') expected2 = os.path.join(data_dir, 'tasks_test_filter_paired_both_pass.out_2.fa') tasks.filter(infile1, outfile1, mate_in=infile2, mate_out=outfile2, minlength=3) self.assertTrue(filecmp.cmp(outfile1, expected1, shallow=False)) self.assertTrue(filecmp.cmp(outfile2, expected2, shallow=False)) os.unlink(outfile1) os.unlink(outfile2) def test_paired_one_pass(self): '''Test filter with paired file one pass''' infile1 = os.path.join(data_dir, 'tasks_test_filter_paired_one_pass.in_1.fa') infile2 = os.path.join(data_dir, 'tasks_test_filter_paired_one_pass.in_2.fa') outfile1 = 'tmp.filter_one_pass_1.fa' outfile2 = 'tmp.filter_one_pass_2.fa' expected1 = os.path.join(data_dir, 'tasks_test_filter_paired_one_pass.out_1.fa') expected2 = os.path.join(data_dir, 'tasks_test_filter_paired_one_pass.out_2.fa') tasks.filter(infile1, outfile1, mate_in=infile2, mate_out=outfile2, both_mates_pass=False, minlength=3) self.assertTrue(filecmp.cmp(outfile1, expected1, shallow=False)) self.assertTrue(filecmp.cmp(outfile2, expected2, shallow=False)) os.unlink(outfile1) os.unlink(outfile2) class TestGetSeqsFlankingGaps(unittest.TestCase): def test_get_seqs_flanking_gaps(self): outfile = 'tmp.seqs_flanking_gaps' tasks.get_seqs_flanking_gaps(os.path.join(data_dir, 'sequences_test_get_seqs_flanking_gaps.fa'), outfile, 3, 3) self.assertTrue(filecmp.cmp(outfile, os.path.join(data_dir, 'sequences_test_get_seqs_flanking_gaps.fa.out'))) os.unlink(outfile) class TestInterleave(unittest.TestCase): def test_interleave(self): '''Check that interleave works as expected''' tmp = 'tmp.interleaved.fa' tasks.interleave(os.path.join(data_dir, 'sequences_test_deinterleaved_1.fa'), os.path.join(data_dir, 'sequences_test_deinterleaved_2.fa'), tmp) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_interleaved.fa'), tmp)) tasks.interleave(os.path.join(data_dir, 'sequences_test_deinterleaved_no_suffixes_1.fa'), os.path.join(data_dir, 'sequences_test_deinterleaved_no_suffixes_2.fa'), tmp, suffix1='/1', suffix2='/2') self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_interleaved_with_suffixes.fa'), tmp)) with self.assertRaises(tasks.Error): tasks.interleave(os.path.join(data_dir, 'sequences_test_deinterleaved_bad_1.fa'), os.path.join(data_dir, 'sequences_test_deinterleaved_bad_2.fa'), tmp) with self.assertRaises(tasks.Error): tasks.interleave(os.path.join(data_dir, 'sequences_test_deinterleaved_bad2_1.fa'), os.path.join(data_dir, 'sequences_test_deinterleaved_bad2_2.fa'), tmp) os.unlink(tmp) class TestMakeRandomContigs(unittest.TestCase): def test_make_random_contigs(self): '''Test make_random_contigs()''' # Can't guarantee same results from random (even using same seed), so # just check sequence names and lengths def files_are_equal(file1, file2): seqs1 = {} seqs2 = {} tasks.file_to_dict(file1, seqs1) tasks.file_to_dict(file2, seqs2) if len(seqs1) != len(seqs2): return False for name in seqs1: seq1 = seqs1[name] seq2 = seqs2[name] if seq1.id != seq2.id: return False if len(seq1) != len(seq2): return False return True tmp = 'tmp.random_contigs.fa' tasks.make_random_contigs(2, 3, tmp) self.assertTrue(files_are_equal(os.path.join(data_dir, 'sequences_test_make_random_contigs.default.fa'), tmp)) tasks.make_random_contigs(2, 3, tmp, prefix='p') self.assertTrue(files_are_equal(os.path.join(data_dir, 'sequences_test_make_random_contigs.prefix-p.fa'), tmp)) tasks.make_random_contigs(2, 3, tmp, first_number=42) self.assertTrue(files_are_equal(os.path.join(data_dir, 'sequences_test_make_random_contigs.first-42.fa'), tmp)) tasks.make_random_contigs(28, 3, tmp, name_by_letters=True) self.assertTrue(files_are_equal(os.path.join(data_dir, 'sequences_test_make_random_contigs.name-by-letters.fa'), tmp)) os.unlink(tmp) class TestMeanLength(unittest.TestCase): def test_mean_length(self): '''Test mean_length''' expected = [3, 2, 3, 4, 4] limits = [1, 2, 3, 4, None] assert len(expected) == len(limits) for i in range(len(expected)): mean = tasks.mean_length(os.path.join(data_dir, 'tasks_test_mean_length.fa'), limit=limits[i]) self.assertEqual(expected[i], mean) class TestMergeToOneSeq(unittest.TestCase): def test_merge_to_one_seq_fa(self): '''Test merge_to_one_seq with fasta''' tmp = 'tmp.merged.fa' tasks.merge_to_one_seq(os.path.join(data_dir, 'sequences_test_merge_to_one_seq.fa'), tmp) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_merge_to_one_seq.merged.fa'), tmp, shallow=False)) os.unlink(tmp) def test_merge_to_one_seq_fq(self): '''Test merge_to_one_seq with fastq''' tmp = 'tmp.merged.fq' tasks.merge_to_one_seq(os.path.join(data_dir, 'sequences_test_merge_to_one_seq.fq'), tmp) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_merge_to_one_seq.merged.fq'), tmp, shallow=False)) os.unlink(tmp) class TestReverseComplement(unittest.TestCase): def test_reverse_complement(self): '''reverse_complement should correctly reverse complement each seq in a file''' tmp = 'tmp.revcomp.fa' tasks.reverse_complement(os.path.join(data_dir, 'sequences_test.fa'), tmp) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_revcomp.fa'), tmp)) os.unlink(tmp) class TestScaffoldsToContigs(unittest.TestCase): def test_scaffolds_to_contigs(self): '''Test scaffolds_to_contigs''' tmp = 'tmp.contigs.fa' tasks.scaffolds_to_contigs(os.path.join(data_dir, 'utils_test_scaffolds.fa'), tmp) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'utils_test_scaffolds.fa.to_contigs.fa'), tmp)) os.unlink(tmp) def test_scaffolds_to_contigs_number_contigs(self): '''Test scaffolds_to_contigs with contig numbering''' tmp = 'tmp.contigs.fa' tasks.scaffolds_to_contigs(os.path.join(data_dir, 'utils_test_scaffolds.fa'), tmp, number_contigs=True) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'utils_test_scaffolds.fa.to_contigs.number_contigs.fa'), tmp)) os.unlink(tmp) class TestSearchForSeq(unittest.TestCase): def test_search_for_seq(self): '''Test that sequence search finds all hits''' tmp = 'tmp.search.fa' tasks.search_for_seq(os.path.join(data_dir, 'sequences_test_search_string.fa'), tmp, 'AGA') self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_search_string.fa.hits'), tmp)) os.unlink(tmp) class TestSequenceTrim(unittest.TestCase): def test_sequence_trim(self): '''Test sequence_trim''' tmp1 = 'tmp.trimmed_1.fa' tmp2 = 'tmp.trimmed_2.fa' in1 = os.path.join(data_dir, 'tasks_test_sequence_trim_1.fa') in2 = os.path.join(data_dir, 'tasks_test_sequence_trim_2.fa') to_trim = os.path.join(data_dir, 'tasks_test_sequences_to_trim.fa') expected1 = os.path.join(data_dir, 'tasks_test_sequence_trim_1.trimmed.fa') expected2 = os.path.join(data_dir, 'tasks_test_sequence_trim_2.trimmed.fa') tasks.sequence_trim(in1, in2, tmp1, tmp2, to_trim, min_length=10, check_revcomp=True) self.assertTrue(filecmp.cmp(expected1, tmp1)) self.assertTrue(filecmp.cmp(expected2, tmp2)) os.unlink(tmp1) os.unlink(tmp2) class ToFastg(unittest.TestCase): def test_to_fastg_ids_set(self): '''Test to_fastg when ids are a set''' infile = os.path.join(data_dir, 'tasks_test_to_fastg.fasta') tmpfile = 'tmp.to_fastg.fastg' expected = os.path.join(data_dir, 'tasks_test_to_fastg.fastg') ids = {'seq2'} tasks.to_fastg(infile, tmpfile, circular=ids) self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) os.unlink(tmpfile) def test_to_fastg_ids_file(self): '''Test to_fastg when ids in a file''' infile = os.path.join(data_dir, 'tasks_test_to_fastg.fasta') tmpfile = 'tmp.to_fastg.fastg' expected = os.path.join(data_dir, 'tasks_test_to_fastg.fastg') ids_file = os.path.join(data_dir, 'tasks_test_to_fastg.ids_to_circularise') tasks.to_fastg(infile, tmpfile, circular=ids_file) self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) os.unlink(tmpfile) class TestTranslate(unittest.TestCase): def test_translate(self): '''Test translate works in each frame''' tmp = 'tmp.translated.fa' for i in range(3): tasks.translate(os.path.join(data_dir, 'sequences_test_translate.fa'), tmp, frame=i) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_translate.fa.frame' + str(i)), tmp)) os.unlink(tmp) class TestTrim(unittest.TestCase): def test_trim(self): '''trim should correctly trim each seq in a file''' tmp = 'tmp.trim.fq' tasks.trim(os.path.join(data_dir, 'sequences_test_untrimmed.fq'), tmp, 2, 1) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_trimmed.fq'), tmp)) os.unlink(tmp) def test_trim_Ns_at_end(self): '''Test Ns at ends of sequences trimmed OK''' tmp = 'tmp.trim.fa' tasks.trim_Ns_at_end(os.path.join(data_dir, 'sequences_test_trim_Ns_at_end.fa'), tmp) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_trim_Ns_at_end.fa.trimmed'), tmp)) os.unlink(tmp) class TestFileToDict(unittest.TestCase): def test_file_to_dict(self): '''check file_to_dict fills dictionary correctly''' d_test = {} d = {} tasks.file_to_dict(os.path.join(data_dir, 'sequences_test.fa'), d_test) for i in range(1,5): d[str(i)] = sequences.Fasta(str(i),'ACGTA') self.assertSequenceEqual(d_test.keys(),d.keys()) for i in range(1,5): key = str(i) self.assertEqual(d_test[key].id, d[key].id) self.assertEqual(d_test[key].seq, d[key].seq) class TestLengthsFromFai(unittest.TestCase): def test_lengths_from_fai(self): '''Check lengths_from_fai gets the length of each seq OK''' d = {} lengths = {str(x):x for x in range(1,5)} tasks.lengths_from_fai(os.path.join(data_dir, 'sequences_test_fai_test.fa.fai'), d) self.assertSequenceEqual(d.keys(), lengths.keys()) for i in d: self.assertEqual(int(i), d[i]) class TestLengthOffsetsFromFai(unittest.TestCase): def test_length_offsets_from_fai(self): '''Test length_offsets_from_fai''' got = tasks.length_offsets_from_fai(os.path.join(data_dir, 'tasks_test_length_offsets_from_fai.fa.fai')) expected = {'seq1': 0, 'seq2': 42, 'seq3': 43} self.assertEqual(expected, got) class TestSplit(unittest.TestCase): def test_split_by_base_count(self): '''Check that fasta/q files get split by base count correctly''' infile = os.path.join(data_dir, 'sequences_test_split_test.fa') outprefix = 'tmp.sequences_test_split_test.fa.test' length2files = {2: ['1','2','3','4'], 3: ['1','2','3'], 4: ['1', '2', '3'], 6: ['1', '2']} for l in length2files: tasks.split_by_base_count(infile, outprefix, l) for x in range(len(length2files[l])): file_index = str(length2files[l][x]) fname = outprefix + '.' + file_index self.assertTrue(filecmp.cmp(fname, infile + '.' + str(l) + '.' + file_index)) os.unlink(fname) # check that limiting the number of files works tasks.split_by_base_count(infile, outprefix, 6, 2) for i in range(1,4): test_file = outprefix + '.' + str(i) self.assertTrue(filecmp.cmp(test_file, os.path.join(data_dir, 'sequences_test_split_test.fa.6.limit2.') + str(i))) os.unlink(test_file) # check big sequence not broken tasks.split_by_base_count(os.path.join(data_dir, 'sequences_test_split_test.long.fa'), outprefix, 2) self.assertTrue(filecmp.cmp(outprefix + '.1', os.path.join(data_dir, 'sequences_test_split_test.long.fa.2.1'))) self.assertTrue(filecmp.cmp(outprefix + '.2', os.path.join(data_dir, 'sequences_test_split_test.long.fa.2.2'))) os.unlink(outprefix + '.1') os.unlink(outprefix + '.2') def test_split_by_fixed_size(self): '''Test fasta/q file split by fixed size''' infile = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa') outprefix = 'tmp.sequences_test_split' tasks.split_by_fixed_size(infile, outprefix, 4, 1) for i in range(1,7,1): correct = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.' + str(i)) test = outprefix + '.' + str(i) self.assertTrue(filecmp.cmp(test, correct)) os.unlink(test) test_coords = outprefix + '.coords' self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.coords'), test_coords)) os.unlink(test_coords) def test_split_by_fixed_size_exclude_Ns(self): infile = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa') outprefix = 'tmp.sequences_test_split' tasks.split_by_fixed_size(infile, outprefix, 4, 1, skip_if_all_Ns=True) for i in range(1,5,1): correct = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.' + str(i)) test = outprefix + '.' + str(i) self.assertTrue(filecmp.cmp(test, correct)) os.unlink(test) test_coords = outprefix + '.coords' self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords'), test_coords)) os.unlink(test_coords) def test_split_by_fixed_size_onefile(self): infile = os.path.join(data_dir, 'sequences_test_split_fixed_size_onefile.fa') tmp_out = 'tmp.sequences_test_split_fixed_size_onefile.fa' expected = os.path.join(data_dir, 'sequences_test_split_fixed_size_onefile.out.fa') tasks.split_by_fixed_size_onefile(infile, tmp_out, chunk_size=3, tolerance=1) self.assertTrue(filecmp.cmp(expected, tmp_out)) os.unlink(tmp_out) def test_split_by_fixed_size_onefile_exclude_Ns(self): infile = os.path.join(data_dir, 'sequences_test_split_fixed_size_onefile.fa') tmp_out = 'tmp.sequences_test_split_fixed_size_onefile.skip_Ns.fa' expected = os.path.join(data_dir, 'sequences_test_split_fixed_size_onefile.skip_Ns.out.fa') tasks.split_by_fixed_size_onefile(infile, tmp_out, chunk_size=3, tolerance=1, skip_if_all_Ns=True) self.assertTrue(filecmp.cmp(expected, tmp_out)) os.unlink(tmp_out) class TestCountSequences(unittest.TestCase): def test_count_sequences(self): '''Check that count_sequences does as expected''' self.assertEqual(2, tasks.count_sequences(os.path.join(data_dir, 'sequences_test_good_file.fq'))) self.assertEqual(4, tasks.count_sequences(os.path.join(data_dir, 'sequences_test.fa'))) self.assertEqual(0, tasks.count_sequences(os.path.join(data_dir, 'sequences_test_empty_file'))) class TestGetIds(unittest.TestCase): def test_get_ids(self): '''Check that IDs extracted correctly from fasta/q file''' tmpfile = 'tmp.ids' tasks.get_ids(os.path.join(data_dir, 'sequences_test.fa'), tmpfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test.fa.ids'), tmpfile)) os.unlink(tmpfile) class TestFastaToFakeQual(unittest.TestCase): def test_fasta_to_fake_qual(self): '''Test fasta_to_fake_qual''' tmpfile = 'tmp.qual' infile = os.path.join(data_dir, 'tasks_test_fasta_to_fake_qual.in.fa') tasks.fastaq_to_fake_qual(infile, tmpfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'tasks_test_fasta_to_fake_qual.out.default.qual'), tmpfile, shallow=False)) os.unlink(tmpfile) tasks.fastaq_to_fake_qual(infile, tmpfile, q=42) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'tasks_test_fasta_to_fake_qual.out.q42.qual'), tmpfile, shallow=False)) os.unlink(tmpfile) class TestFastaToFastq(unittest.TestCase): def test_fasta_to_fastq(self): '''Check fasta_to_fastq converts files as expected''' tasks.fasta_to_fastq(os.path.join(data_dir, 'sequences_test.fa'), os.path.join(data_dir, 'sequences_test.fa.qual'), 'tmp.fq') self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test.fasta_to_fastq.fq'), 'tmp.fq')) with self.assertRaises(tasks.Error): tasks.fasta_to_fastq(os.path.join(data_dir, 'sequences_test.fa'), os.path.join(data_dir, 'sequences_test.fa.qual.bad'), 'tmp.fq') os.unlink('tmp.fq') class TestReplaceBases(unittest.TestCase): def test_sequences_replace_bases(self): '''Check that fasta file gets all bases replaced OK''' tmpfile = 'tmp.replace_bases.fa' tasks.replace_bases(os.path.join(data_dir, 'sequences_test_fastaq_replace_bases.fa'), tmpfile, 'T', 'X') self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_fastaq_replace_bases.expected.fa'), tmpfile)) os.unlink(tmpfile) class TestSortBySize(unittest.TestCase): def test_sort_by_size(self): '''Test sort_by_size''' infile = os.path.join(data_dir, 'tasks_test_sort_by_size.in.fa') tmpfile = 'tmp.sorted.fa' tasks.sort_by_size(infile, tmpfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'tasks_test_sort_by_size.out.fa'), tmpfile, shallow=False)) tasks.sort_by_size(infile, tmpfile, smallest_first=True) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'tasks_test_sort_by_size.out.rev.fa'), tmpfile, shallow=False)) os.unlink(tmpfile) class TestStripIlluminaSuffix(unittest.TestCase): def test_strip_illumina_suffix(self): '''Check illumina suffixes stripped correctly off read names''' tmpfile = 'tmp.stripped.fa' tasks.strip_illumina_suffix(os.path.join(data_dir, 'sequences_test_strip_illumina_suffix.fq'), tmpfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_strip_illumina_suffix.fq.stripped'), tmpfile)) os.unlink(tmpfile) class TestStatsFromFai(unittest.TestCase): def test_stats_from_fai_nonempty(self): '''Test task stats_from_fai non-empty file''' infile = os.path.join(data_dir, 'tasks_test_stats_from_fai.in.fai') got = tasks.stats_from_fai(infile) expected = { 'longest': 10, 'shortest': 1, 'N50': 4, 'mean': 4.2, 'number': 5, 'total_length': 21 } self.assertEqual(expected, got) def test_stats_from_fai_empty(self): '''Test task stats_from_fai empty file''' infile = os.path.join(data_dir, 'tasks_test_stats_from_fai.in.empty.fai') got = tasks.stats_from_fai(infile) expected = { 'longest': 0, 'shortest': 0, 'N50': 0, 'mean': 0, 'number': 0, 'total_length': 0 } self.assertEqual(expected, got) class TestToBoulderio(unittest.TestCase): def test_to_boulderio(self): '''Test task to_boulderio''' tmpfile = 'tmp.boulder' tasks.to_boulderio(os.path.join(data_dir, 'tasks_test_to_boulderio.in.fa'), tmpfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'tasks_test_to_boulderio.out.boulder'), tmpfile, shallow=False)) os.unlink(tmpfile) class TestToFasta(unittest.TestCase): def test_to_fasta(self): '''Test to_fasta''' tmpfile = 'tmp.to_fasta' infiles = [ 'sequences_test_good_file.fq', 'sequences_test_gffv3.gff', 'sequences_test_gffv3.no_FASTA_line.gff', 'sequences_test.embl', 'sequences_test.gbk', 'sequences_test_phylip.interleaved', 'sequences_test_phylip.interleaved2', 'sequences_test_phylip.sequential' ] infiles = [os.path.join(data_dir, x) for x in infiles] expected_outfiles = [x + '.to_fasta' for x in infiles] for i in range(len(infiles)): tasks.to_fasta(infiles[i], tmpfile) self.assertTrue(filecmp.cmp(expected_outfiles[i], tmpfile)) tasks.to_fasta(os.path.join(data_dir, 'sequences_test.fa'), tmpfile, line_length=3) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test.line_length3.fa'), tmpfile)) tasks.to_fasta(os.path.join(data_dir, 'sequences_test_strip_after_whitespace.fa'), tmpfile, strip_after_first_whitespace=True) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_strip_after_whitespace.fa.to_fasta'), tmpfile)) os.unlink(tmpfile) def test_to_fasta_strip_after_whitespace_non_unique(self): '''Test strip_after_whitespace with non-unique names''' tmpfile = 'tmp.strip_after_whitespace.fa' infile = os.path.join(data_dir, 'sequences_test.to_fasta.strip_after_whitespace_non_unique.in.fa') expected = os.path.join(data_dir, 'sequences_test.to_fasta.strip_after_whitespace_non_unique.out.fa') with self.assertRaises(tasks.Error): tasks.to_fasta(infile, tmpfile, strip_after_first_whitespace=True, check_unique=True) tasks.to_fasta(infile, tmpfile, strip_after_first_whitespace=True, check_unique=False) self.assertTrue(filecmp.cmp(tmpfile, expected, shallow=False)) os.unlink(tmpfile) def test_to_fasta_strip_after_whitespace_unique(self): '''Test strip_after_whitespace with unique names''' tmpfile = 'tmp.strip_after_whitespace.fa' infile = os.path.join(data_dir, 'sequences_test.to_fasta.strip_after_whitespace_unique.in.fa') expected = os.path.join(data_dir, 'sequences_test.to_fasta.strip_after_whitespace_unique.out.fa') tasks.to_fasta(infile, tmpfile, strip_after_first_whitespace=True, check_unique=True) self.assertTrue(filecmp.cmp(tmpfile, expected, shallow=False)) os.unlink(tmpfile) class TestToUniqueByID(unittest.TestCase): def test_to_unique_by_id(self): '''Test to_unique_by_id()''' tmpfile = 'tmp.unique_by_id.fa' tasks.to_unique_by_id(os.path.join(data_dir, 'sequences_test_to_unique_by_id.fa'), tmpfile) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_to_unique_by_id.fa.out'), tmpfile)) os.unlink(tmpfile) class TestToFastaUnion(unittest.TestCase): def test_to_fasta_union(self): '''Test to_fasta_union''' tmpfile = 'tmp.to_fasta_union' tasks.to_fasta_union(os.path.join(data_dir, 'sequences_test_to_fasta_union.in.fa'), tmpfile, seqname='testname') self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_to_fasta_union.out.fa'), tmpfile, shallow=False)) os.unlink(tmpfile) if __name__ == '__main__': unittest.main() Fastaq-3.14.0/pyfastaq/tests/utils_test.py000066400000000000000000000062131276201573500205730ustar00rootroot00000000000000#!/usr/bin/env python3 import sys import os import filecmp import unittest from pyfastaq import utils modules_dir = os.path.dirname(os.path.abspath(utils.__file__)) data_dir = os.path.join(modules_dir, 'tests', 'data') class TestUtils(unittest.TestCase): def test_write_and_read(self): '''open_file_write() and open_file_read() should do the right thing depending gzipped or not''' for filename in ['utils.tmp', 'utils.tmp.gz', 'utils.tmp.bgz']: f = utils.open_file_write(filename) for i in range(3): print(i, file=f) utils.close(f) counter = 0 f = utils.open_file_read(filename) for line in f: self.assertEqual(counter, int(line.strip())) counter += 1 utils.close(f) os.unlink(filename) f = utils.open_file_read('-') self.assertEqual(sys.stdin, f) f = utils.open_file_write('-') self.assertEqual(sys.stdout, f) def test_raise_exception(self): '''open_file_write() and open_file_read() should raise an exception when can't do the opening''' with self.assertRaises(utils.Error): utils.open_file_read('this_file_is_not_here_so_throw_error') with self.assertRaises(utils.Error): utils.open_file_read('this_file_is_not_here_so_throw_error.gz') with self.assertRaises(utils.Error): utils.open_file_read(os.path.join(data_dir, 'utils_test_not_really_zipped.gz')) with self.assertRaises(utils.Error): utils.open_file_write(os.path.join('not_a_directory', 'this_file_is_not_here_so_throw_error')) with self.assertRaises(utils.Error): utils.open_file_write(os.path.join('not_a_directory', 'this_file_is_not_here_so_throw_error.gz')) def test_file_transpose(self): '''Test that file_transpose() does what it should''' infile = os.path.join(data_dir, 'utils_test_file_transpose.txt') tmp_out = 'utils_test_file_transpose.tmp' correct_file = os.path.join(data_dir, 'utils_test_file_transposed.txt') utils.file_transpose(infile, tmp_out) self.assertTrue(filecmp.cmp(tmp_out, correct_file)) os.unlink(tmp_out) def test_system_call(self): '''Test that system call appears to work and die as it should''' test_file = os.path.join(data_dir, 'utils_test_system_call.txt') tmp_out = 'utils_test_syscall.tmp' utils.syscall('cat ' + test_file + ' > ' + tmp_out) self.assertTrue(filecmp.cmp(tmp_out, test_file)) os.unlink(tmp_out) with self.assertRaises(utils.Error): utils.syscall('thisisveryunlikelytoebarealcommandandshouldthrowerror') utils.syscall('echo "this is not the right string" > ' + tmp_out) self.assertFalse(filecmp.cmp(tmp_out, test_file)) os.unlink(tmp_out) s = utils.syscall_get_stdout('echo bingo') self.assertListEqual(["bingo"], s) with self.assertRaises(utils.Error): utils.syscall_get_stdout('thisisveryunlikelytoebarealcommandandshouldthrowerror') if __name__ == '__main__': unittest.main() Fastaq-3.14.0/pyfastaq/utils.py000066400000000000000000000043451276201573500163760ustar00rootroot00000000000000import os import sys import subprocess import shlex class Error (Exception): pass def open_file_read(filename): if filename == '-': f = sys.stdin elif filename.endswith('.gz'): # first check that the file is OK according to gunzip retcode = subprocess.call('gunzip -t ' + filename, shell=True) if retcode != 0: raise Error("Error opening for reading gzipped file '" + filename + "'") # now open the file f = os.popen('gunzip -c ' + filename) else: try: f = open(filename) except: raise Error("Error opening for reading file '" + filename + "'") return f def open_file_write(filename): if filename == '-': f = sys.stdout elif filename.endswith('.gz'): if not os.path.exists(os.path.abspath(os.path.dirname(filename))): raise Error("Error opening for writing gzipped file '" + filename + "'") try: f = os.popen('gzip -9 -c > ' + filename, 'w') except: raise Error("Error opening for writing gzipped file '" + filename + "'") else: try: f = open(filename, 'w') except: raise Error("Error opening for writing file '" + filename + "'") return f def close(filehandle): if filehandle not in [sys.stdout, sys.stderr]: filehandle.close() def file_transpose(f_in, f_out, sep_in=None, sep_out='\t'): rows = [] f = open_file_read(f_in) for line in f: rows.append(line.rstrip().split(sep_in)) close(f) columns_out = max([len(x) for x in rows]) for r in rows: r += ['.'] * (columns_out - len(r)) f = open_file_write(f_out) for i in range(columns_out): print(sep_out.join([str(rows[x][i]) for x in range(len(rows))]), file=f) close(f) def syscall(cmd): retcode = subprocess.call(cmd, shell=True) if retcode != 0: raise Error("Error in system call. Command was:\n" + cmd) def syscall_get_stdout(cmd): try: out = subprocess.Popen(shlex.split(cmd), stdout=subprocess.PIPE).communicate()[0].decode('utf-8').rstrip() return out.split('\n') except: raise Error('Error in system call. I tried to run:\n' + str(cmd)) Fastaq-3.14.0/scripts/000077500000000000000000000000001276201573500145155ustar00rootroot00000000000000Fastaq-3.14.0/scripts/fastaq000077500000000000000000000100041276201573500157150ustar00rootroot00000000000000#!/usr/bin/env python3 import argparse import sys tasks = { 'acgtn_only': 'Replace every non acgtnACGTN with an N', 'add_indels': 'Deletes or inserts bases at given position(s)', 'caf_to_fastq': 'Converts a CAF file to FASTQ format', 'capillary_to_pairs': 'Converts file of capillary reads to paired and unpaired files', 'chunker': 'Splits sequences into equal sized chunks', 'count_sequences': 'Counts the sequences in input file', 'deinterleave': 'Splits interleaved paired file into two separate files', 'enumerate_names': 'Renames sequences in a file, calling them 1,2,3... etc', 'expand_nucleotides': 'Makes every combination of degenerate nucleotides', 'fasta_to_fastq': 'Convert FASTA and .qual to FASTQ', 'filter': 'Filter sequences to get a subset of them', 'get_ids': 'Get the ID of each sequence', 'get_seq_flanking_gaps': 'Gets the sequences flanking gaps', 'interleave': 'Interleaves two files, output is alternating between fwd/rev reads', 'make_random_contigs': 'Make contigs of random sequence', 'merge': 'Converts multi sequence file to a single sequence', 'replace_bases': 'Replaces all occurrences of one letter with another', 'reverse_complement': 'Reverse complement all sequences', 'scaffolds_to_contigs': 'Creates a file of contigs from a file of scaffolds', 'search_for_seq': 'Find all exact matches to a string (and its reverse complement)', 'sequence_trim': 'Trim exact matches to a given string off the start of every sequence', 'split_by_base_count': 'Split multi sequence file into separate files', 'sort_by_size': 'Sorts sequences in length order', 'strip_illumina_suffix': 'Strips /1 or /2 off the end of every read name', 'to_boulderio': 'Converts to Boulder-IO format, used by primer3', 'to_fasta': 'Converts a variety of input formats to nicely formatted FASTA format', 'to_fake_qual': 'Make fake quality scores file', 'to_mira_xml': 'Create an xml file from a file of reads, for use with Mira assembler', 'to_orfs_gff': 'Writes a GFF file of open reading frames', 'to_perfect_reads': 'Make perfect paired reads from reference', 'to_random_subset': 'Make a random sample of sequences (and optionally mates as well)', 'to_tiling_bam': 'Make a BAM file of reads uniformly spread across the input reference', 'to_unique_by_id': 'Remove duplicate sequences, based on their names. Keep longest seqs', 'translate': 'Translate all sequences in input nucleotide sequences', 'trim_contigs': 'Trims a set number of bases off the end of every contig', 'trim_ends': 'Trim fixed number of bases of start and/or end of every sequence', 'trim_Ns_at_end': 'Trims all Ns at the start/end of all sequences', 'version': 'Print version number and exit', } def print_usage_and_exit(): print('Usage: fastaq [options]', file=sys.stderr) print('\nTo get minimal usage for a command use:\nfastaq command', file=sys.stderr) print('\nTo get full help for a command use one of:\nfastaq command -h\nfastaq command --help\n', file=sys.stderr) print('\nAvailable commands:\n', file=sys.stderr) max_task_length = max([len(x) for x in list(tasks.keys())]) for task in sorted(tasks): print('{{0: <{}}}'.format(max_task_length).format(task), tasks[task], sep=' ', file=sys.stderr) sys.exit(1) if len(sys.argv) == 1 or sys.argv[1] in ['-h', '-help', '--help']: print_usage_and_exit() task = sys.argv.pop(1) if task not in tasks: print('Task "' + task + '" not recognised. Cannot continue.\n', file=sys.stderr) print_usage_and_exit() exec('import pyfastaq.runners.' + task) exec('pyfastaq.runners.' + task + '.run("' + tasks[task] + '")') Fastaq-3.14.0/setup.py000066400000000000000000000013341276201573500145410ustar00rootroot00000000000000import glob from setuptools import setup, find_packages setup( name='pyfastaq', version='3.14.0', description='Script to manipulate FASTA and FASTQ files, plus API for developers', packages = find_packages(), author='Martin Hunt', author_email='mh12@sanger.ac.uk', url='https://github.com/sanger-pathogens/Fastaq', scripts=glob.glob('scripts/*'), test_suite='nose.collector', tests_require=['nose >= 1.3'], license='GPLv3', classifiers=[ 'Development Status :: 4 - Beta', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3 :: Only', 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', ], )