[Bioperl-l] extracting 'comments' from gff-ver 2

[Charles Hauser]

Malcom,

I see why this should work, but I get warning that tag value sequence does not exist?


    while($feature = $gffio->next_feature()) {
	if($feature->primary_tag eq 'gene') {
	    print 
		"Target ", $feature->seqname,"\n",
		"Query ", ($feature->each_tag_value('sequence'))[0],"\n";
	}
    }




------------- EXCEPTION  -------------
MSG: asking for tag value that does not exist sequence
STACK Bio::SeqFeature::Generic::each_tag_value /usr/lib/perl5/site_perl/5.6.1/Bio/SeqFeature/Generic.pm:507
STACK main::GFF gff_parser.pl:55
STACK toplevel gff_parser.pl:22


On Fri, 2003-04-04 at 10:42, Cook, Malcolm wrote:
> Charles,
> 
> try:
> 	($feature->each_tag_value('sequence'))[0]
> where you have 
> 	$feature->comments
> 
> -Malcolm Cook
> 
> > -----Original Message-----
> > From: Charles Hauser [mailto:chauser at duke.edu]
> > Sent: Friday, April 04, 2003 9:21 AM
> > To: BioPerl-List
> > Subject: [Bioperl-l] extracting 'comments' from gff-ver 2
> > 
> > 
> > I am trying to generate a plot of the distribution of ESTs on genomic
> > scaffolds using the GFF output from exonerate.  I need to grab the
> > clone_id  in the comments field '833005F02.y1'. 
> > 
> > the method $feature->comments does not exist, how can I access these
> > data?  
> > 
> > -regards
> > 
> > Charles
> > 
> > 
> > 
> > 
> > use Bio::Tools::GFF;
> > <snip>
> > my $gffio = Bio::Tools::GFF->new(-fh => \*FH,
> > 				 -gff_version => 2);
> > my $feature;
> > while($feature = $gffio->next_feature()) {
> >     if($feature->primary_tag eq 'gene') {
> > 	print 
> > 	    $feature->seqname,  "\n",
> > 	    $feature->comments,  "\n";
> > 
> > 
> > 
> > ##gff-version 2
> > ##source-version exonerate:est2genome 0.6.7
> > ##date 2003-03-24
> > ##type DNA
> > #
> > #
> > # seqname source feature start end score strand frame attributes
> > #
> > scaffold_1	exonerate:est2genome	gene	367897	368609	
> > 1884	+	.	gene_id	1	;	sequence	
> > 833005F02.y1	;	gene_orientation	
> > +	;
> > 
> > 
> > 
> > 
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> >