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

[morgarws@mh.us.sbphrd.com]

Tried that ... didn't work =>
-------------------- WARNING ---------------------
MSG:  
---------------------------------------------------
-------------------- WARNING ---------------------
MSG:  
---------------------------------------------------
Use of uninitialized value at /bioinfo/apps/perl5.005_03/lib/site_perl/5.005/Bi
o/Search/HSP/BlastHSP.pm line 487, <GEN1> chunk 3360.
Illegal division by zero at /bioinfo/apps/perl5.005_03/lib/site_perl/5.005/Bio/
Search/HSP/BlastHSP.pm line 487, <GEN1> chunk 3360.
DB: gbfunc
Hit: [gb|AC079226.7|AC079226] [Homo sapiens BAC clone RP11-18D7 from 4, 
complete
 sequence]
      [0.99992] [184032] [0.99992]

I forwarded the wu blast output file to Jason ... didn't think the list would 
like getting 143k worth of blast ;-)

Regards,

Bill Morgart

> In the meantime, try creating the SearchIO object with '-format' => 'psiblast'.
> This uses a different parser which should support WU-BLAST. 
> 
> Steve
> 
> --- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> > 
> > 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
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> > 
> > -- 
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> 
> 
> =====
> Steve Chervitz
> sac@bioperl.org
> 
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