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

[Leonardo Marino-Ramirez]

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
> >
>
>