[Biopython-dev] comments on BLAT parser

[Brandon King]

Hi Yair,
    Thanks for the update! That should come in handy!

-Brandon King

Yair Benita wrote:

>Hi All,
>Jeff Chang and I made a few changes to the NCBIstandalone module and you may
>now use it to parse BLAT output. Just a few comments on that:
>
>1. BLAT can be run either using the BLAT program or the gfServer gfClient
>programs. The testing was done using gfServer-gfClient version 32.
>
>2. Use the option -out=blast to get the output file in BLAST format.
>
>3. When using BLAT to compare a DNA query to a DNA database, everything
>works perfectly well. However, when comparing a protein query to a
>translated DNA database, there is a bug in the BLAST output. The subject
>coordinates are wrong if the hit is on the opposite strand. This bug is
>known and will be fixed in the next release of BLAT. For now, if you compare
>proteins to a translated DNA database, use the psl format.
>
>Below is an example for parsing the blat output (note that the query_end and
>sbjct_end have also been added to the NCBIstandalone module).
>
>Yair
>
>##################################################
>from Bio.Blast import NCBIStandalone
>
>BlatFile = "blat_output.txt"
>blast_out = open(BlatFile,'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
>        
>    print "Query used:", b_record.query
>    
>    for hitX in b_record.alignments:
>        print "\t Target: ", hitX.title
>
>        for hspX in hitX.hsps:
>            print "\t\tQuery location: %s to %s" % ( hspX.query_start,
>                                                        hspX.query_end)
>            print "\t\ttarget location: %s to %s" % ( hspX.sbjct_start,
>                                                        hspX.sbjct_end)
>            print "\t\tstrand:", hspX.strand
>            print "\t\tscore: %s" % hspX.score
>            print "\t\tbits: %s" % hspX.bits
>            print "\t\texpect: %s" % hspX.expect
>            print "\t\tidentity:", hspX.identities
>            print "\t\t" + "-"*20
>
>blast_out.close()
>##################################################
>
>
>
>_______________________________________________
>Biopython-dev mailing list
>Biopython-dev at biopython.org
>http://biopython.org/mailman/listinfo/biopython-dev
>
>
>  
>