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