Mercurial > repos > rhpvorderman > shm_csr

annotate summary_to_fasta.py @ 2:72d68e2e1fd3 draft

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"planemo upload commit a8565b413cbe0ef70bc22994ecdd48b400ba6185"
author rhpvorderman
date Fri, 05 Nov 2021 14:43:13 +0000
parents 64d74ba01a7c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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1 import argparse
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2
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3 parser = argparse.ArgumentParser()
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4 parser.add_argument("--input", help="The 1_Summary file of an IMGT zip file")
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5 parser.add_argument("--fasta", help="The output fasta file")
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6
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7 args = parser.parse_args()
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8
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9 infile = args.input
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10 fasta = args.fasta
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11
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12 with open(infile, 'r') as i, open(fasta, 'w') as o:
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13 first = True
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14 id_col = 0
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15 seq_col = 0
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16 no_results = 0
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17 no_seqs = 0
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18 passed = 0
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19 for line in i:
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20 splt = line.split("\t")
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21 if first:
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22 id_col = splt.index("Sequence ID")
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23 seq_col = splt.index("Sequence")
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24 first = False
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25 continue
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26 if len(splt) < 5:
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27 no_results += 1
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28 continue
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30 ID = splt[id_col]
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31 seq = splt[seq_col]
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32
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33 if not len(seq) > 0:
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34 no_seqs += 1
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35 continue
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37 o.write(">" + ID + "\n" + seq + "\n")
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38 passed += 1
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39
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40 print("No results:", no_results)
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41 print("No sequences:", no_seqs)
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42 print("Written to fasta file:", passed)