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

[Leonardo Marino-Ramirez]

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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

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