[Bioperl-l] bl2seq, get high scoring matches

[Tobias Thierer]

Hi,

I would like to use bl2seq to get high scoring local
alignments of sequence pair subsequences. So, following
the documentation, I say:

   $factory = Bio::Tools::Run::StandAloneBlast->new(
              'program' => 'blastn',
              'outfile' => 'bl2seq.out');
   $report = $factory->bl2seq($seqA, $seqB);


So that $report is now a reference to a BPbl2seq object
containing the blast report. As I understand the
documentation, there are two ways of proceeding now. Both
yield errors if there is no high scoring match of the
two sequences. More specifically:

Try #1: read the result from bl2seq.out
=======================================

 my $in = Bio::AlignIO->new(-file => "<bl2seq.out", 
                            -format =>'bl2seq');
 my $align = $in->next_aln;

If bl2seq.out contains no hits (sample file attached to this
eMail), the code above produces the following error:

------------- EXCEPTION  -------------
MSG:  No hit object found for bl2seq report 
 
STACK Bio::Tools::BPbl2seq::next_feature
path-to-bioperl-1.0.2/Bio/Tools/BPbl2seq.pm:232
STACK Bio::AlignIO::bl2seq::next_aln
path-to-bioperl-1.0.2/Bio/AlignIO/bl2seq.pm:122
STACK Bio::AlignIO::READLINE
path-to-bioperl-1.0.2/Bio/AlignIO.pm:463
STACK main::bl2seqAlign process.pl:60
STACK toplevel process.pl:70

----------------------------------

although the documentation at

 http://doc.bioperl.org/releases/bioperl-1.0.2/Bio/AlignIO/bl2seq.html

states that next_aln returns 0 upon end of file or
error. Is this a bug or am I doing something wrong?



Try #2: proceed with the BPbl2seq object referenced by $report
==============================================================

[...do something with $report->sbjctName etc....]

while (my $hsp = $report->next_feature) {
   # (...)
}


In my case, this yields:

Can't call method "nextHSP" on unblessed reference at
/(...)/bioperl-1.0.2/Bio/Tools/BPbl2seq.pm line 237, <GEN10>
line 31


So: am I just too dumb to understand the documentation and use
BioPerl (I'm quite new to it) or is this a bug in BioPerl?
Any help would be appreciated.

Thanks in advance,

     Tobias Thierer

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