bioperl MapTiling error

Question

[Shyam]

Hi I wrote a script for parsing blast output and get some of the statistics. But while I run the script:

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. Bioperl v1.007001 and BLAST+ 2.2.31

EDIT: Only throws this error when asking to report the methods for 'subject' or 'hit'. For 'query' only, everything works just as expected.

Thank you shyam

[Ram]

I'd print out to stdout the query that's causing this error, then examine a GUI based BLAST output to check on the HSPs.

[Shyam]

I tried with different queries with different number of HSPs, it works if I use only the 'query' instead of 'subject' for

my $sub_length_tiling = $tiling->length('subject');

I emailed Dr Jensen the developer for this module. Will update when I heard back from him.

Thanks for the suggestion.

Answer 1

[Mark A. Jensen]

Hi Shyam - I just ran across this by chance, sorry if I didn't see your email.

It has been a long time since I looked at this code, but my guess is that your subject sequence is being matched in its reverse complement (i.e., in the context "m_"), but the default is "p_" in this case. Try

 $tiling->length('subject', 'exact', 'm_')

and see if it succeeds.

The Perl error is a bug on my part; it shouldn't completely bork like that. If you could create an issue at https://github.com/bioperl/bioperl-live/issues that would be great.

MAJ