[Bioperl-l] RE: :SeqIO HOWTO

Barry Moore bmoore at genetics.utah.edu
Thu Nov 3 12:10:59 EST 2005


The HOWTOs are generally example based, and thus are not comprehensive
documentation.  The primary documentation for the details of any module
is found in POD within that module.  You can access that by running
perldoc on the actual perl module (perldoc
/usr/lib/perl5/site_perl/5.8.5/Bio/Seq.pm on my system) or browse
through the module documentation online (for bioperl 1.4 currently) at

For instance, point you browser to
http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html click on
"Methods", choose Description under display_name, and you'll get:

 Title   : display_name
 Usage   : $string    = $obj->display_name()
 Function: A string which is what should be displayed to the user
           the string should have no spaces (ideally, though a cautious
           user of this interface would not assumme this) and should be
           less than thirty characters (though again, double checking
           this is a good idea)

           This is aliased to display_id().
 Returns : A scalar


> -----Original Message-----
> From: chen li [mailto:chen_li3 at yahoo.com]
> Sent: Thursday, November 03, 2005 6:55 AM
> To: Barry Moore
> Subject: Bio::SeqIO HOWTO
> Dear Dr. Moore,
> One more question: which parts of the HOWTOs  describe
> the methods for
> alphabet/description/display_name/length/seq?
> > print $seq->alphabet,"\n";
> > print $seq->description,"\n";
> > print $seq->display_name,"\n";
> > print $seq->length,"\n";
> > print $seq->seq,"\n";
> Li
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