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

[Cook, Malcolm]

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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