Re: error whiling using MapTiling

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Re: error whiling using MapTiling

Ghana
The error is thrown only for the subject or the hit methods. If I use only query methods the scripts runs fine and reports as expected. 

Any ideas on resolving this?

Thanks
Ghana

On Friday, February 17, 2017 at 10:07:49 AM UTC-6, Ghana wrote:
Hi I wrote a script for parsing blast output and get some of the statistics. But while I run the script:

#!/usr/local/bin/perl


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

my $infile = $ARGV[0];
my $in = Bio::SearchIO->new(-format => 'blast', -file => $infile);
my $result = $in->next_result;

my $hit;
while ($hit = $result->next_hit){
my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
                my $query_length_tiling = $tiling->length('query');
my $sub_length_tiling = $tiling->length('subject');
my $qid = $tiling->frac_identical('query');
my $qcov = $tiling->percent_identity('query');
                print $query_length_tiling."\t".$sub_length_tiling."\t".$qid."\t".$qcov;
print "\n";
}

I am getting this error


--------------------- WARNING ---------------------

MSG: No HSPS present for type 'hit' in context 'p_' for this hit

---------------------------------------------------

Can't use an undefined value as an ARRAY reference at /Library/Perl/5.18/Bio/Search/Tiling/MapTiling.pm line 1135, <GEN1> line 600.


Please help me to resolve this error. 

Thank you
Ghana


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