[Bioperl-l] Problem with Bio::DB::GeneBank

[IIZUKA Soichi]

hi,

I have a problem with Bio::DB::GeneBank.
get_Stream_by_acc() dosen't seem to return correct Bio::SeqIO object.

$ perl -MBio::Seq -MBio::SeqIO -MBio::DB::GeneBank
my $gb = new Bio::DB::GeneBank(-retrievaltype => "tempfile", -format =>
"Fasta");
my $seqio = $gb->get_Stream_by_acc(["some", "accession", "numbers"]);
my $seq = $seqio->next_seq();
print $seq->display_id();
^D

This test code returned follwoing error.
-------------------- EXCEPTION --------------------
MSG: Attempting to set the sequence to [<HTML] which does not look healthy
STACK Bio::PrimarySeq::seq /usr/share/perl5/Bio/PrimarySeq.pm:243
STACK Bio::PrimarySeq::new /usr/share/perl5/Bio/PrimarySeq.pm:218
STACK Bio::Seq::new /usr/share/perl5/Bio/Seq.pm:132
STACK Bio::SeqIO::fasta::next_primary_seq
/usr/share/perl5/Bio/SeqIO/fasta.pm:130
STACK Bio::SeqIO::fasta::next_seq /usr/share/perl5/Bio/SeqIO/fasta.pm:85
STACK toplevel:3
---------------------------------------------------

I have also tested get_Seq_by_acc(), but it resulted in the same error.

How can I get correct Bio::SeqIO object by get_Stream_by_acc() method?

Thanks.

--
IIZUKA Soichi
mailto: j6498007@ed.noda.sut.ac.jp