[Bioperl-l] sequence object question

Jason Stajich jason at bioperl.org
Sun Feb 3 18:51:21 EST 2008


It is 'get_SeqFeatures'
http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1

Deobfuscator:
http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio 
%3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq
http://bioperl.org/cgi-bin/deob_detail.cgi? 
method=Bio::Seq::get_SeqFeatures

HOWTO:
http://bioperl.org/wiki/HOWTO:Feature-Annotation


On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote:

> hi,
> here is the problem i'm facing.
>
> i parse a genbank file with the statement:
> my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format =>
> 'GenBank');
> while (my $seq_obj= $gb_stream->next_seq){
> .....
>
> }
>
> presumably $seq_obj is a Bio::Seq::RichSeq object.
>
> now, when I try:
> my $feat_obj($seq_obj->getSeqFeatures){
> .....
> }
> i get an error message: Can't locate object method "getSeqFeatures"  
> via
> package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11.
>
>
> on reading docs I find that Bio::Seq::RichSeq does not have a  
> getSeqFeatures
> method.
> but, RIchSeq is a child of the Seq class, which HAS a  
> getSeqFeatures method
> (i presume this method is also inherited by the RichSeq class).
>
> so, why am i getting an error message and how do i go about getting  
> the
> features within each genbank file?
>
> appreciate any pointers.
>
> TIA.
>
> anjan
>
> -- 
> ANJAN PURKAYASTHA, PhD.
> Senior Computational Biologist
> ==========================
>
> 1101 King Street, Suite 310,
> Alexandria, VA 22314.
> 703.518.8040 (office)
> 703.740.6939 (mobile)
>
> email:
> anjan at vbi.vt.edu;
> anjan.purkayastha at gmail.com
>
> http://www.vbi.vt.edu
>
> ==========================
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