[Bioperl-l] Bio::SearchIO

Wed Aug 4 12:23:23 EDT 2004

Hi Jason,

I am listing my code below... I tried it with the blast results (blastx)
annexed to this msg... the error msg I get is:

Query= 366
2
0
28
46
201
437
174
247

Query= 366
Can't call method "query" on an undefined value at parser.pl line 22,
<GEN1> line 8164.

Curiously the script worked well (without any warning/error) parsing
another file resulting from a tblastx search.

Thanks in advance, Alberto

*****

CODE:

#!/usr/bin/perl

use lib "/usr/local/bioperl14";
use Bio::SearchIO;

  $searchio = new Bio::SearchIO ('-format' => 'blast',
                                 '-file'   => 'clusters.blast');

  while ($result = $searchio->next_result) {
     $query_name = $result->query_name(); 
     $cluster_id = $query_name;

     while ($hit = $result->next_hit) {
       ($gi) = $hit->name =~ /gi\|(\d+)\|/;
       $hsp = $hit->next_hsp;
       $accession = $hit->accession;
       $description = $hit->description();
       $expect = $hit->significance();
       $score = $hit->raw_score();
       $length = $hit->length();
print "Query= $cluster_id\n";
       $query_frame = $hsp->query->frame;
print "$query_frame\n";
       $hit_frame = $hsp->hit->frame;
print "$hit_frame\n";
       $identical=$hsp->num_identical;
print "$identical\n";
       $conserved=$hsp->num_conserved;
print "$conserved\n";
       $query_start=$hsp->start('query');
print "$query_start\n";
       $query_end=$hsp->end('query');
print "$query_end\n";
       $hit_start=$hsp->start('hit');
print "$hit_start\n";
       $hit_end=$hsp->end('hit');
print "$hit_end\n\n";

       }

  }

On Wed, 2004-07-28 at 10:10, Jason Stajich wrote:
> good - so Alberto - we need some way to replicate your problem.  What
> version of bioperl are you using, etc....
> 
> -jason
> 
> On Wed, 28 Jul 2004, Brian Osborne wrote:
> 
> > Jason,
> >
> > Yes, $hsp->end('query') works using the latest bioperl-live code.
> >
> > Brian O.
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at portal.open-bio.org
> > [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason Stajich
> > Sent: Tuesday, July 27, 2004 10:04 AM
> > To: davila
> > Cc: bioperl-l at bioperl.org
> > Subject: Re: [Bioperl-l] Bio::SearchIO
> >
> > It should still work.
> >
> > You may try:
> > $hsp->query->start
> > $hsp->query->end
> >
> > $hsp->hit->start
> > $hsp->hit->end
> >
> > This should be equivalent with
> > $hsp->start('hit'), $hsp->end('hit'), ... etc
> >
> > But it is possible that something has been changed in the object layer
> > that broke this.  I'm not really sure since it should be in the tests...
> >
> > if you can post code + an example BLAST file as a bug report at
> > http://bugzilla.bioperl.org which demonstrates the problem we'll have a
> > look.
> >
> > -jason
> >
> > On Tue, 27 Jul 2004, davila wrote:
> >
> > > I was using the last year a Blast parser with the following lines:
> > >
> > >        $query_start=$hsp->start('query');
> > >        $query_end=$hsp->end('query');
> > >        $hit_start=$hsp->start('hit');
> > >        $hit_end=$hsp->end('hit');
> > >
> > > however it is no longer working and I had to comment them in order to have
> > the parser working. If there were any changes, how I could now catch the
> > "query_start", "query_end", "hit_start" and "hit_end" from the Blast results
> > ?
> > >
> > > Thanks in advance, Alberto
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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