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

Barry Moore barry.moore at genetics.utah.edu
Thu Feb 8 14:35:03 EST 2007


Sheri-

The Bio::SeqFeature::Generic object has a 'strand' method, so you can  
just call strand on the CDS (or any other) feature like this.

   my @features = grep { $_->primary_tag eq 'CDS' } $seq- 
 >get_SeqFeatures();
   for my $feature (@features) {
	  my $strand = $feature->strand;
  }

Barry

On Feb 8, 2007, at 10:42 AM, Sheri Simmons wrote:

> 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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