Mercurial > repos > davidvanzessen > shm_csr
view summary_to_fasta.py @ 35:744e5e2e3556 draft
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author | davidvanzessen |
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date | Fri, 16 Dec 2016 10:00:10 -0500 |
parents | c33d93683a09 |
children | 729738462297 |
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import argparse parser = argparse.ArgumentParser() parser.add_argument("--input", help="The 1_Summary file of an IMGT zip file") parser.add_argument("--fasta", help="The output fasta file") args = parser.parse_args() infile = args.input fasta = args.fasta with open(infile, 'r') as i, open(fasta, 'w') as o: first = True id_col = 0 seq_col = 0 no_results = 0 no_seqs = 0 passed = 0 for line in i: splt = line.split("\t") if first: id_col = splt.index("Sequence ID") seq_col = splt.index("Sequence") first = False continue if len(splt) < 5: no_results += 1 continue ID = splt[id_col] seq = splt[seq_col] if not len(seq) > 0: no_seqs += 1 continue o.write(">" + ID + "\n" + seq + "\n") passed += 1 print "No results:", no_results print "No sequences:", no_seqs print "Written to fasta file:", passed