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'