[Bioperl-l] SearchIO and WU-BLAST ....

[Jason Stajich]

The code was best tested on NCBI blast output - can you send a blast
report which causes this behavior and I'll see what patch is needed.
Your version of wu-blast is helpful too.

-j
On Tue, 26 Mar 2002 morgarws@mh.us.sbphrd.com wrote:

>
> I'm having a problem with the SearchIO module and parsing WashU Blast output
> .. The SearchIO parser is skipping groups of HSPs that have been combined,
> i.e. the only HSPs that are found are those where the P(N) is P(1). Is this a
> known problem with SearchIO or have I missed something (likely)? Here is some
> code that doesn't work for hits that have more than 1 HSP combined:
>
> use Bio::SearchIO;
>
> my $searchio = Bio::SearchIO->new('-format' => 'blast',
> 				  '-file' => 'gbfunc-test.fasta.out');
> while (my $result = $searchio->next_result()) {
>
> # Get info about the entire report
>     print "DB: " .  $result->database_name . "\n";
>
> # get info about each hit
>     my ($hit, $hsp);
>     while ($hit = $result->next_hit) {
> 	my $hit_name = $hit->name ;
> 	my $hit_description = $hit->description;
> 	my $hit_rawscore = $hit->raw_score;
> 	my $hit_length = $hit->length;
> 	my $hit_significance = $hit->significance;
> 	print "Hit: [$hit_name] [$hit_description]\n      [$hit_rawscore]
> [$hit_length] [$hit_significance]\n";
>
> # get info about the hsp(s) of the hit
> 	while ($hsp = $hit->next_hsp()) {
> 	    my $hsp_part;
> 	    my $hsp_percent_id = $hsp->percent_identity();
> 	    my $hsp_length = $hsp->length();
> 	    print "  HSP: [$hsp_percent_id] [$hsp_length]\n";
> 	}
>     }
> }
>
> Regards,
>
> Bill Morgart
> morgarws@Molbio.sbphrd.com
>
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu