Mercurial > repos > iuc > humann_join_tables
view test-data/test-db/metaphlan-db/customizemapping.py @ 3:6c3271894a95 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 32d4c566afe55179531fdd106dc5a996cc09bbb1
author | iuc |
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date | Wed, 29 Mar 2023 20:02:22 +0000 |
parents | fd7ebf31b030 |
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#!/usr/bin/env python # -*- coding: utf-8 -*- # Script to generate a extract a custom mapping file from input mapping file. # Mostly used for a reduced-size demo data generation. import argparse from pathlib import Path if __name__ == '__main__': # Read command line parser = argparse.ArgumentParser(description='Customize HUMAnN utility mapping') parser.add_argument('--in_mapping', help="Path to mapping file to reduce") parser.add_argument('--features', help="Path to tabular file with features to keep in first column") parser.add_argument('--elements', help="Path to tabular file with elements to keep in other columns") parser.add_argument('--out_mapping', help="Path to reduced mapping file") args = parser.parse_args() in_mapping_fp = Path(args.in_mapping) feature_fp = Path(args.features) element_fp = Path(args.elements) out_mapping_fp = Path(args.out_mapping) # extract features to keep features = set() with open(feature_fp, 'r') as feature_f: for line in feature_f.readlines(): features.add(line.split("\t")[0]) print(features) # extract elements to keep elements = set() with open(element_fp, 'r') as element_f: for line in element_f.readlines(): elements.add(line.split("\t")[0]) print(elements) # write mapping for features to keep while keeping only elements with open(in_mapping_fp, 'r') as in_mapping_f: with open(out_mapping_fp, 'w') as out_mapping_f: for line in in_mapping_f.readlines(): l_split = line.split("\t") feat = l_split[0] if feat in features: to_write = [feat] for e in l_split[1:]: if e in elements: to_write.append(e) out_mapping_f.write("%s\n" % '\t'.join(to_write))