[shrujan]

Thank you andrews its getting now..if any problem persists i'll ask you stay in touch...thank you once again

[shrujan]

#!/usr/bin/perl -w

use strict;
use Bio::Tools::BPlite;
use Bio::Tools::Run::StandAloneBlast;
use Bio:B::SwissProt;

my $blastfile = '/home/data/problemdata/problem8/ecoli1_ecoliaa.bls';

my @params = ('database' => 'nr',
'outfile' => 'blast1.out',
'_READMETHOD' => 'BPlite',
'program' => 'blastp');
my $swissdb= new Bio:B::SwissProt();
my $blastfactory = new Bio::Tools::Run::StandAloneBlast(@params);
my $seq = $swissdb->get_Seq_by_acc('KPY1_ECOLI');
my $report = $blastfactory->blastall($seq);


#my $report = new Bio::Tools::BPlite(-file => $blastfile);


print "report is ", $report->query, "\n";
print "db is ", $report->database, "\n";;
SUBJECT: while(my $sbjct = $report->nextSbjct) {
print "subject name is ", $sbjct->name, "\n";

HSP: while (my $hsp = $sbjct->nextHSP) {
if( $hsp->P() > 1 ) { next SUBJECT;}
print "\t score = ", $hsp->score;
$hsp->bits;
$hsp->percent;
print " p value is ", $hsp->P, "\n";
$hsp->match;
$hsp->positive;
$hsp->length;
$hsp->querySeq;
$hsp->sbjctSeq;
$hsp->homologySeq;
$hsp->query->start;
$hsp->query->end;
$hsp->subject->start;
$hsp->subject->end;
$hsp->subject->seqname;

#$hsp->subject->overlaps($exon);
}
}


while i am executing this perl program..in command prompt it is showing the following error...
C:\Perl\bin>fasta.pl
Can't locate Bio/Tools/BPlite.pm in @INC (@INC contains: C:/Perl/site/lib C:/Per
l/lib .) at C:\Perl\bin\fasta.pl line 4.
BEGIN failed--compilation aborted at C:\Perl\bin\fasta.pl line 4.


please guide me....

[simonandrews]

BPlite is deprecated in the latest BioPerl releases. You should use the SearchIO modules instead now.

[shrujan]

can u list out those modules..please..so that i can solve it...thank you

[simonandrews]

I put a link in the last post. Go look at that and it talks you through how to do this with the SearchIO modules.