[Bioperl-l] Bio/SearchIO/Writer/GbrowseGFF.pm

[Alexie Papanicolaou]

hello all,

1) I was wondering if you would you know what this error means and had 
time to help...

Use of uninitialized value in concatenation (.) or string at 
/usr/local/share/perl/5.8.8/Bio/SearchIO/Writer/GbrowseGFF.pm line 287

line 287 is
            else {
                $tags{'Target'} = "$prefix:$seqname $qpmax $qpmin";
            }

this is the header
# $Id: GbrowseGFF.pm,v 1.15.4.1 2006/10/02 23:10:27 sendu Exp $
#
# BioPerl module Bio::SearchIO::Writer::GbrowseGFF.pm


this is how I call it... ( 2.6.18-6-amd64, x86_64, perl, v5.8.8, 
bioperl: tried with both 1.5.2_102 from cvs and checked out svn version 
today)

use Bio::SearchIO::Writer::GbrowseGFF;
use Bio::SearchIO;
if ($program eq "blastn"){
#my $out_gff  = new Bio::SearchIO(-writer => $writer_gff,
 my $out_gff = new Bio::SearchIO(-output_format  => 'GbrowseGFF',
                        -output_cigar   => 1,
                        -output_signif  => 1,
                        -file   => ">$infile.$query.blast.gff");
#my $out_gff_whole  = new Bio::SearchIO(-writer => $writer_gff,
 my $out_gff_whole = new Bio::SearchIO(-output_format  => 'GbrowseGFF',
                        -output_cigar   => 1,
                        -output_signif  => 1,
                           -file   => ">>$infile.blast.gff");
$out_gff->write_result($result);
$out_gff_whole->write_result($result);
}



Where $result is a blast result...

The aim is to parse a multi-query blast report and split it into 
different queries and make another file with all the queries. I'm sure 
i'm forgetting something but I can't figure what...

The GFF file is produced, but I do get the error above...

2) Finally, there is a small bug but I don't think it comes from this 
module? The id attribute is printed out e.g iD=match_sequence31 with iD 
wrongly capitalised...

many thanks for your time
alexie

-- 
--
Alexie Papanicolaou
Entomology
Max Planck Institute for Chemical Ecology
Hans Knoell Str 8
Jena 07745
Germany
Email apapanicolaou at ice.mpg.de
Tel +493641571561