[Bioperl-l] [Bioperl-guts-l] Location of sequence text extractions (fwd)

[Jason Stajich]

$feature->spliced_seq;

http://www.bioperl.org/Core/Latest/FAQ.html#Q5.5
Q5.5: How do I get the complete spliced nucleotide sequence from the CDS
section?

A: You can use the spliced_seq() method. For example:

my $seq_obj = $db->get_Seq_by_id($gi);
foreach my $feat ( $seq_obj->top_SeqFeatures ) {
   if ( $feat->primary_tag eq 'CDS' ) {
      my $cds_obj = $feat->spliced_seq;
      print "CDS sequence is ",$cds_obj->seq,"\n";
   }
}


This is implemented in Bio::SeqFeatureI

-jason
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Mon, 07 Jul 2003 11:35:09 -0500
From: John A. Crow <crow at mail.ahc.umn.edu>
To: bioperl-guts-l at bioperl.org
Cc: crow at ccgb.umn.edu
Subject: [Bioperl-guts-l] Location of sequence text extractions


-- 
I'm a recent addition to the bioperl developers, and still
navigating blindly.

I am trying to locate where the action is for Bio::Seq objects
for actually extracting and returning the sequence text via
$seqobj->seq() method.

In particular, if I have a sequence *feature* like a gene or
CDS, then where are the guts that process the complex
complement(), join(), gap(), etc., specifications of the feature
location?

Thanks for any guidance!
 - John

_______________________________________________________________
John A. Crow
crow at ccgb.umn.edu

Center for Computational Genomics & Bioinformatics
University of Minnesota
Mayo MC 43
420 Delaware Street S.E.
Minneapolis, MN 55455 USA
http://ccgb.umn.edu/~crow
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