Question: bioperl MapTiling error
0
gravatar for Shyam
21 months ago by
Shyam120
United States
Shyam120 wrote:

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

blast bioperl • 577 views
ADD COMMENTlink modified 16 months ago by Mark A. Jensen0 • written 21 months ago by Shyam120

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.

ADD REPLYlink written 20 months ago by RamRS19k

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.

ADD REPLYlink modified 20 months ago • written 20 months ago by Shyam120
0
gravatar for Mark A. Jensen
16 months ago by
Mark A. Jensen0 wrote:

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

ADD COMMENTlink written 16 months ago by Mark A. Jensen0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1921 users visited in the last hour