Mercurial > repos > bvalot > fasta_filter_0_1

annotate fasta_filter_to_accession.py @ 0:bc23da9d464c draft default tip

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planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
author bvalot
date Tue, 14 Jun 2022 08:15:55 +0000
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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1 #!/usr/bin/env python3
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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2 # -*- coding: utf-8 -*-
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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4 """Return a filter fasta file for list of accession"""
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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6 import argparse
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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7 import sys
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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9 from Bio import SeqIO
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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11 desc = "Filter a fasta file based on ."
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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12 command = argparse.ArgumentParser(
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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13 prog="fasta_filter_to_accession",
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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14 description=desc,
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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15 usage="%(prog)s [options] fasta accessions",
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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16 )
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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17 command.add_argument(
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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18 "-o",
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19 "--output",
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20 default=sys.stdout,
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21 type=argparse.FileType("w"),
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22 nargs="?",
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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23 help="Output result to, default:stdout",
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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24 )
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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25 command.add_argument("fasta", type=argparse.FileType("r"), help="Fasta file to filter")
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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26 command.add_argument(
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27 "access",
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28 metavar="accessions",
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29 type=str,
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30 nargs="+",
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31 help="List of accession to extract",
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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32 )
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33
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34 if __name__ == "__main__":
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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35 """Performed job on execution script"""
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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36 args = command.parse_args()
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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37 output = args.output
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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38 access = set(args.access)
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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39 for seq in SeqIO.parse(args.fasta, "fasta"):
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40 if seq.id in access:
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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41 SeqIO.write(seq, output, "fasta")
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42 access.remove(seq.id)
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43 if len(access) > 0:
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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44 sys.stderr.write("Accessions not found : " + str(" - ").join(access) + "\n")