annotate fasta_affixer.py @ 12:6b7d31026d1c draft

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author petr-novak
date Tue, 04 Feb 2020 08:38:22 -0500
parents a4cd8608ef6b
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python3
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2 ''' fasta affixer - adding prefixes and suffixes to fasta sequence names'''
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3 import argparse
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4
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5 parser = argparse.ArgumentParser()
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6 parser.add_argument("-f", "--fasta", type=str, help="fasta file")
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7 parser.add_argument("-o", "--output", type=str, help="output fasta file")
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8 parser.add_argument(
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9 "-p", "--prefix",
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10 type=str, help="prefix to be added to names")
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11 parser.add_argument(
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12 "-s", "--suffix",
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13 type=str, help="suffix to be added",
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14 default='')
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15 parser.add_argument("-n",
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16 "--nspace",
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17 type=int,
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18 help="number of spaces to ignore",
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19 default='0')
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20
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21 args = parser.parse_args()
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22
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23 with open(args.fasta, "r") as f, open(args.output, "w") as out:
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24 for oneline in f:
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25 if oneline == "":
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26 continue
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27 if not oneline:
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28 break
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29 if oneline[0] == ">":
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30 header = " ".join(oneline.split()[:1 + args.nspace])
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31 header_out = header[0] + args.prefix + header[1:] + args.suffix + "\n"
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32 out.write(header_out)
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33 else:
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34 out.write(oneline)
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