[Bioperl-l] sequence object question

ANJAN PURKAYASTHA anjan.purkayastha at gmail.com
Sun Feb 3 12:10:49 EST 2008


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
==========================

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email:
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anjan.purkayastha at gmail.com

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