Mercurial > repos > rreumerman > snptools
comparison gbk_to_fasta.py @ 4:bd5692103d5b draft
Uploaded
| author | rreumerman |
|---|---|
| date | Fri, 05 Apr 2013 05:00:40 -0400 |
| parents | |
| children |
comparison
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| 3:a808647d7312 | 4:bd5692103d5b |
|---|---|
| 1 import sys | |
| 2 | |
| 3 if len(sys.argv) < 3: | |
| 4 exit("Not enough arguments passed, pleas provide names of input- and output file") | |
| 5 | |
| 6 input_name = sys.argv[1] | |
| 7 output_name = sys.argv[2] | |
| 8 | |
| 9 from Bio import GenBank | |
| 10 | |
| 11 try: seq_record = GenBank.RecordParser().parse(open(input_name)) | |
| 12 except: exit("Error reading %s, check file correctness." % input_name) | |
| 13 | |
| 14 try: out_file = open(output_name, 'w') | |
| 15 except IOError as e: | |
| 16 exit("Error trying to open '%s': {1}".format(e.errno, e.strerror)) | |
| 17 | |
| 18 accession = definition = '' | |
| 19 if seq_record.accession[0] != '': accession = '|gb|'+seq_record.accession[0] | |
| 20 if seq_record.definition != '': definition = '|'+seq_record.definition | |
| 21 | |
| 22 out_file.write(">gi|%s%s%s\n" % (seq_record.gi,accession,definition)) | |
| 23 | |
| 24 i = 0 | |
| 25 while i < len(seq_record.sequence): | |
| 26 out_file.write(seq_record.sequence[i:i+70]+"\n") | |
| 27 i += 70 | |
| 28 | |
| 29 out_file.close() |