Mercurial > repos > drosofff > cherry_pick_fasta

annotate cherry_pick_fasta.py @ 9:fb7f833cce11 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author drosofff
date Wed, 09 Nov 2016 11:31:47 -0500
parents 726b1e233a08
children
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3 """
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4 Chery pick of fasta sequences satisfying a query string in their header/name
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5 """
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6
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7 import argparse
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8
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9 def Parser():
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10 the_parser = argparse.ArgumentParser(
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11 description="Cherry pick fasta sequences")
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12 the_parser.add_argument(
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13 '--input', action="store", type=str, help="input fasta file")
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14 the_parser.add_argument(
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15 '--query-string', dest="query_string", action="store", type=str,
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16 help="header containing the string will be extracted as well as the corresponding sequence")
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17 the_parser.add_argument(
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18 '--output', action="store", type=str, help="output fasta file")
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19 args = the_parser.parse_args()
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20 return args
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21
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22 def __main__():
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23 """ main function """
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24 args = Parser()
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25 search_term = args.query_string
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26 CrudeFasta = open (args.input, "r").read()
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27 Output = open (args.output, "w")
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28 FastaListe = CrudeFasta.split(">")
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29 for sequence in FastaListe:
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30 if search_term in sequence:
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31 print >> Output, ">%s" % sequence.rstrip()
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32 Output.close()
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33
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34
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35 if __name__ == "__main__":
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36 __main__()