[NORDNS] [Bioperl-l] Bio::Seq documentation?

[Brian Osborne]

Wes,

If you look at the "Docs" page,
http://www.bioperl.org/Core/Latest/modules.html , you'll see the link to the
Complete Module Documentation,
http://doc.bioperl.org/releases/bioperl-1.2.3/. That lower left frame is a
list of all the modules, select "Seq" to get to the Bio::Seq page. One
problem with the software that creates these individual module pages is that
it sometime sticks a lot of the useful documentation at the bottom of the
page, particularly evident in the case of Seq.pm.

You could also have gotten to this Bio::Seq page from the bptutorial, which
has a brief section on Bio::Seq.

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Wes Barris
Sent: Wednesday, September 24, 2003 12:46 AM
To: Bioperl Mailing List
Subject: [NORDNS] [Bioperl-l] Bio::Seq documentation?

Hi,

According to the bioperl documentation the Bio::SeqIO genbank method
"next_seq" returns a "Bio::Seq" object.  Where is the documentation
for a "Bio::Seq" object?  In the documentation on the bioperl web site,
if you click on "bioperl-1.2.3::Bio::Seq" I see the following list:

BaseSeqProcessor
EncodedSeq
LargePrimarySeq
LargeSeq
PrimaryQual
PrimedSeq
QualI
RichSeq
RichSeqI
SeqBuilder
SeqFactory
SeqFastaSpeedFactory
SeqWithQuality
SequenceTrace
TraceI

Which one of these do I look under to find out information about what
is returned by "next_seq"?

What I am trying to do is to parse a genbank file and find out the
sequence direction (3 prime or 5 prime).  What I have done is this,
but I am trying to find out if there is a better "built-in" way to do this:

    if ($seq->description =~ /3'/) {
       $direction = '3prime';
       }
    elsif ($seq->description =~ /5'/) {
       $direction = '5prime';
       }

--
Wes Barris
E-Mail: Wes.Barris at csiro.au


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