view gbk_to_fasta.py @ 4:bd5692103d5b draft

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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()