Re: error whiling using MapTiling

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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