Mercurial > repos > iuc > ivar_filtervariants
view completemask.py @ 12:8f8df367470d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
author | iuc |
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date | Mon, 13 Feb 2023 17:28:58 +0000 |
parents | 7fe36019c073 |
children |
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#!/usr/bin/env python import sys if __name__ == '__main__': with open(sys.argv[1]) as i: getmasked_output = i.readline().strip() if not getmasked_output: print() print('No affected primer binding sites found!') else: masked_primers = getmasked_output.split('\t') with open(sys.argv[2]) as i: amplicon_data = [line.strip().split('\t') for line in i] masked_complete = [] for primer in masked_primers: for amplicon in amplicon_data: if primer in amplicon: masked_complete += amplicon result = '\t'.join(sorted(set(masked_complete))) print() print('Removing reads primed with any of:') print(result) with open(sys.argv[1], 'w') as o: o.write(result + '\n')