[Bioperl-l] bioperl newbie needs help with extracting cds info

Kevin Brown Kevin.M.Brown at asu.edu
Thu Feb 8 14:11:50 EST 2007


When you extract the features, just look at the strand method on the
returned sequence to find out.

@features = $seq->all_SeqFeatures;
# sort features by their primary tags
for my $f (@features)
{
	my $tag = $f->primary_tag;
	if ($tag eq 'CDS')
	{
		print $f->strand ."\n";
	}
} 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Sheri Simmons
> Sent: Thursday, February 08, 2007 10:42 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] bioperl newbie needs help with 
> extracting cds info
> 
> Hi,
> I'm a newbie to BioPerl so apologies if this is a very basic 
> question. I am trying to parse GenBank files with the goal of 
> creating concatenated gene lists in nucleic acid or amino 
> acid format. It is working fine, except for one thing: I need 
> to create gene labels incorporating information on whether 
> the gene is on the complementary strand or not ("complement" 
> in the CDS tag). How can I get Bioperl to tell me whether the 
> CDS tag value includes the word "complement"?
> 
> Thanks
> Sheri
> 
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