[Bioperl-l] Length of a sequence.

Chris Fields cjfields at uiuc.edu
Fri Sep 8 10:31:27 EDT 2006


Nick,

It should be '$seq_object->length()'.

If you need a list of the methods for a particular Bioperl object type, I
recommend the Deobfuscator:

http://www.bioperl.org/wiki/Deobfuscator

http://bioperl.org/cgi-bin/deob_interface.cgi


Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Staffa, Nick (NIH/NIEHS) [C]
> Sent: Friday, September 08, 2006 9:14 AM
> To: bioperl-l
> Subject: [Bioperl-l] Length of a sequence.
> 
> Wondering why I'm having trouble finding out how to get the total length
> of a sequence.
> I am doing wonderfully parsing all the features information.
> y'd think this would be simple.
> What's the best thing to do?
> 
> 
> use Bio::SeqIO;
> #       Get the sequence
> ...
> $seqio_object = Bio::SeqIO->new(-file => "$filename" );
> $seq_object = $seqio_object->next_seq;
> >>> What's the magic code to put HERE????<<<<<<<<<<<<<<<<<<<
> print "Sequence $fileroot has length $len\n";
> #       Get the features as an array of objects
> #       This seems to get them all. Makes an array of objects.
> my @features = $seq_object->get_SeqFeatures(); # just top level
> 
> 
> 
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
> 
> 
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> Bioperl-l at lists.open-bio.org
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