Mercurial > repos > rreumerman > snptools
view gbk_to_fasta.py @ 7:8de0ffc2166f draft default tip
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author | rreumerman |
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date | Mon, 10 Jun 2013 09:40:54 -0400 |
parents | bd5692103d5b |
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import sys if len(sys.argv) < 3: exit("Not enough arguments passed, pleas provide names of input- and output file") input_name = sys.argv[1] output_name = sys.argv[2] from Bio import GenBank try: seq_record = GenBank.RecordParser().parse(open(input_name)) except: exit("Error reading %s, check file correctness." % input_name) try: out_file = open(output_name, 'w') except IOError as e: exit("Error trying to open '%s': {1}".format(e.errno, e.strerror)) accession = definition = '' if seq_record.accession[0] != '': accession = '|gb|'+seq_record.accession[0] if seq_record.definition != '': definition = '|'+seq_record.definition out_file.write(">gi|%s%s%s\n" % (seq_record.gi,accession,definition)) i = 0 while i < len(seq_record.sequence): out_file.write(seq_record.sequence[i:i+70]+"\n") i += 70 out_file.close()