Exalted Monks!

I need your help with script troubleshooting. I am using a BioPerlmodule without really understanding Object Oriented Programming. My input file is at http://bit.ly/1LXIS26. And the script I am using to process it is below if you scroll down. The output it generates is missing information for the ID - 'Brdisv1ABR21023941m', not sure why. WIth other input files, sometimes no IDs are missing, but other times, exactly 1 ID is missing.

Furthermore, warning on STDOUT reads as below - not sure what it means!

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

MSG: unrecognized line (2): CS -HHHHS-HHHHHHHHTTS-HHHHHHHTTT-HHHHHHHCT- HHH HH

What am I doing wrong with using the Bio::SearchIO BioPerl module, or something else? THANKS! 

#!/usr/bin/perl
# HMMER_parser.pl

use strict;
use warnings;

# downloaded from https://metacpan.org/pod/Bio::SearchIO::hmmer

use Bio::SearchIO;

my $source = shift @ARGV;
my @out;

open(IN, '<', $source) or die "Can't read source file $source : $!\n";


my $in = Bio::SearchIO->new(-format => 'hmmer',
                           -file   => $source);
while( my $result = $in->next_result ) {
    # this is a Bio::Search::Result::HMMERResult object
    print $result->query_name(), " for HMM ", $result->hmm_name(), "\n
+";
    while( my $hit = $result->next_hit ) {
        push @out, $hit->name(), "\t";
        while( my $hsp = $hit->next_hsp ) {
            push @out, $hsp->length(), "\n";
        }
    }
}

close IN;

my @split_input_name=split('.out',$source,);
my $destination = $split_input_name[0]."FBD_H2_Dom-only.IDsLens";

open(OUT, '>', $destination) or die "Can't read source file $destinati
+on : $!\n";
print OUT @out;
close OUT;

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In reply to Learning BioPerl/OOP and script troubleshooting help by onlyIDleft

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