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comparison genericize_db.py @ 0:41990c43f371 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
author galaxyp
date Wed, 10 Jul 2024 06:14:45 +0000
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-1:000000000000 0:41990c43f371
1 #!/usr/bin/env python3
2 #
3 # Prefixes sequence headers in the input FASTA file that are not formatted according to the UniProt, NCBI, or ENSEMBL formats with '>generic|' to avoid being misinterpreted by Philosopher.
4 #
5
6 import re
7 import sys
8
9 input_db_file = sys.argv[1]
10 output_db_file = sys.argv[2]
11
12
13 def sub_header(line):
14 return re.sub(r'^>(?!sp\||tr\||db\||AP_|NP_|YP_|XP_|WP_|ENSP|UniRef|nxp|generic)', '>generic|', line)
15
16
17 with open(input_db_file) as in_file, open(output_db_file, 'w') as out_file:
18 for line in in_file:
19 out_file.write(sub_header(line))