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

[Chris Fields]

I have run into a number of problems with the GbrowseGFF module myself  
(I think I committed the ID fix, actually).  It works but needs  
revision and needs better conformity with GFF3.

You can post (1) as a bug and well look into it when we can.  It's  
possible (depending on how extensive the fix is) this may have to wait  
until 1.7.

chris

On Mar 4, 2008, at 6:03 AM, Alexie Papanicolaou wrote:

> 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
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign