MSG: Start/stop out of range | Bio::Search::Tiling::MapTiling

Thiago Venancio <[email protected]>
Newsgroups gmane.comp.lang.perl.bio.general
Message-ID <[email protected]>
Hi all,

By running the following code in the BLAST report attached I get the 
following error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Start/stop out of range [824, 1141]
STACK: Error::throw
STACK: Bio::Root::Root::throw 
/usr/local/share/perl/5.20.1/Bio/Root/Root.pm:449
STACK: Bio::Search::HSP::HSPI::matches_MT 
/usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTileUtils.pm:583
STACK: Bio::Search::Tiling::MapTiling::_calc_stats 
/usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTiling.pm:1163
STACK: Bio::Search::Tiling::MapTiling::length 
/usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTiling.pm:508
STACK: Bio::Search::Tiling::MapTiling::num_aligned 
/usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTiling.pm:694
STACK: Bio::Search::Tiling::MapTiling::frac_aligned 
/usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTiling.pm:668
STACK: blParse.pl:40
-----------------------------------------------------------

I used the following code:

use strict;
use warnings;
use Bio::SearchIO;
use Bio::Search::Tiling::MapTiling;

my $searchio = Bio::SearchIO->new( -format => 'blast',
   -file   => shift );

my $gene;

while ( my $result = $searchio->next_result() ) {

    $result->query_name =~ /(\S+_\S+)_i/;
    my $g = $1;

    while( my $hit = $result->next_hit ) {
        
my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
my $hsp    = $hit->next_hsp;

my $st    = $hsp->query->strand == "1" ? "p" : "m";
my $frame = $hsp->query->frame;
 my $context = $st.$frame;

print $tiling->frac_aligned('query', 'exact', $context)."\n";
    }
}

Any clues on how to deal with this error ?

Thanks in advance.
Thiago

_______________________________________________
Bioperl-l mailing list
[email protected]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
lmpx.com only provides a reader for public news (NNTP) servers. It is not affiliated with the servers or forums shown here and is not responsible for the content of articles, which is written by their respective authors.