[Bioperl-l] Bug in Bio::Tools::BPlite::HSP.pm ?

[Jason Eric Stajich]

Because you are running a bioperl 0.7 which is an earlier release of the
code.  We package it up at specific points in time and release it.  This
is then distributed to CPAN and can be installed either from there or by
downloading the tarball from ftp://bioperl.org/pub/DIST.

The bioperl-live code (accessible via CVS) is always the most up-to-date
version of the code, however this also means it is not always stable.  You
can choose to use one or the other or both, but you will need to
understand how to point your PERL5LIB to the correct place, etc.

You can browse the code, see differences between versions, etc at
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/?cvsroot=bioperl
from a web browser.

-jason

On Wed, 5 Sep 2001, Leonardo Marino-Ramirez wrote:

> Jason,
>
> Thanks for the bugfix. I just checked the bioperl-live branch doing:
>
> cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl checkout
> bioperl-live
>
> and this is the output of
>
> head /usr/lib/perl5/site_perl/5.005/Bio/Tools/BPlite/Sbjct.pm
> # $Id: Sbjct.pm,v 1.11 2001/02/26 20:02:44 jason Exp $
>
> I just downloaded the file directly from the http://cvs.bioperl.org/ site
> and the script is working fine. Thanks!
>
> How come bioperl-live have Sbjct.pm,v 1.11 instead of 1.18?
>
> Thanks, Leonardo
>
> On Wed, 5 Sep 2001, Jason Eric Stajich wrote:
>
> > This is because your report has the following in the scoreline
> > Expect(2) = e-32
> > rather than
> > Expect = e-32
> >
> > I have patched this on bioperl live (CVS head).
> > Patch is also below.  Thanks for reporting it.  If you cannot patch the
> > code yourself you can
> > a) do a cvs checkout of bioperl code and put this dir in your PERL5LIB
> > b) run sed 's/Expect(2)/Expect/' REPORTNAME | perl blastscript.pl
> >
> > HTH
> > -jason
> >
> > --begin
> > Index: Bio/Tools/BPlite/Sbjct.pm
> > ===================================================================
> > RCS file:
> > /home/repository/bioperl/bioperl-live/Bio/Tools/BPlite/Sbjct.pm,v
> > retrieving revision 1.17
> > retrieving revision 1.18
> > diff -r1.17 -r1.18
> > 1c1
> > < # $Id: Sbjct.pm,v 1.17 2001/08/25 12:11:11 lapp Exp $
> > ---
> > > # $Id: Sbjct.pm,v 1.18 2001/09/05 14:43:12 jason Exp $
> > 136,137c136
> > <   if (not defined $p) {($p) = $scoreline =~ /Expect =\s+(\S+)/}
> > <
> > ---
> > >   if (not defined $p) {(undef, $p) = $scoreline =~ /Expect(\(\d+\))? =\s+(\S+)/}
> > --end
> >
> > On Wed, 5 Sep 2001, Leonardo Marino-Ramirez wrote:
> >
> > > Hello,
> > >
> > > I am trying to get e-values from blast reports using the
> > > Bio::Tools::BPlite module. So far I am able to get pretty much all the
> > > atributes from the HSP object.
> > >
> > > I am using a standard script to get e-values:
> > >
> > > #!/usr/bin/perl
> > >
> > > use Bio::Tools::BPlite;
> > >
> > > my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);
> > >
> > > my $query = $report->query;
> > > @tmp = split ' ', $query; $qn = $tmp[0];
> > > my $database = $report->database;
> > >
> > >
> > > while(my $sbjct = $report->nextSbjct) {
> > >     my $blast_hit = $sbjct->name;
> > >     @tmp = split /\|/, $blast_hit; $gi = $tmp[1];
> > >     print "\ngi is $gi\nquery is $qn\n";
> > >     while(my $hsp = $sbjct->nextHSP) {
> > >         $sc = $hsp->bits; print "score is $sc\n";
> > >         $ev = $hsp->P; print "e-value is $ev\n";
> > >    }
> > > }
> > >
> > > The problem is that when I am reading a report that has
> > >
> > > 3 different e-values the only one that is parsed correctly is the third
> > > one.
> > >
> > > My output of the script above looks like this:
> > >
> > > gi is 1787829
> > > query is EBO9901A09.Seq
> > > score is 290
> > > e-value is 1
> > > score is 29.6
> > > e-value is 1
> > >
> > > gi is 1787636
> > > query is EBO9901A09.Seq
> > > score is 123
> > > e-value is 1
> > > score is 29.6
> > > e-value is 1
> > >
> > > gi is 1787403
> > > query is EBO9901A09.Seq
> > > score is 58.2
> > > e-value is 7e-10
> > >
> > >
> > > What is the problem?
> > >
> > > uname -a
> > > Linux tofu.tamu.edu 2.2.12-20smp #1 SMP Mon Sep 27 10:34:45 EDT 1999 i686
> > > unknow
> > > n
> > >
> > >
> > > Thanks, Leonardo
> > >
> >
> >
>

-- 
Jason Stajich
Duke University
jason.stajich@duke.edu