merge_mapping_files.py – Merge mapping files¶
Description:
This script provides a convenient interface for merging mapping files which contain data on different samples.
Usage: merge_mapping_files.py [options]
Input Arguments:
Note
[REQUIRED]
- -m, --mapping_fps
- The input mapping files in a comma-separated list
- -o, --output_fp
- The output mapping file to write
[OPTIONAL]
- -n, --no_data_value
- Value to represent missing data (i.e., when all fields are not defined in all mapping files) [default: no_data]
- --case_insensitive
- If present the headers will be merged case insensitivly and transformed to upper case [default: False]
Output:
The result of this script is a merged mapping file (tab-delimited).
Example:
Merge two mapping files into a new mapping file (merged_mapping.txt). In cases where a mapping field is not provided for some samples, add the value ‘Data not collected’.
merge_mapping_files.py -m map_controls.txt,map_fasting.txt -o merged_mapping.txt -n 'Data not collected'