[Bioperl-l] sequence object question

ANJAN PURKAYASTHA anjan.purkayastha at gmail.com
Sun Feb 3 23:00:33 EST 2008


Thanks a lot!


On Feb 3, 2008 6:51 PM, Jason Stajich <jason at bioperl.org> wrote:

> 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
> >
> > ==========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


-- 
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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