[Biopython-dev] [Bug 1929] Extra reference in BLASTPGP plain text output

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1929





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2006-01-17 06:19 -------
Created an attachment (id=263)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=263&action=view)
Example BLASTAPGP output, plain text

Script from the bug reporter:

#!/usr/bin/python

import os
from Bio.Blast import NCBIStandalone

blast_out = open('blast.output2', 'r')
b_parser = NCBIStandalone.BlastParser()
b_iterator = NCBIStandalone.Iterator(blast_out, b_parser)
while 1:
        b_record = b_iterator.next()
        if b_record is None:
                break

        for alignment in b_record.alignments:
                for hsp in alignment.hsps:
                        if hsp.expect < 0.04:
                                print 'sequence:' , alignment.title




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