[Bioperl-l] bioperl genbank output is different than web?

[Jason Stajich]

Actually grab the official bioperl 1.5.1 release.  ReleaseCandidates  
are archived but not in the main DIST directory anymore:
http://news.open-bio.org/archives/2005_10.html#000084


On Oct 16, 2005, at 7:21 AM, Barry Moore wrote:

> Sam-
>
> This is a known bug in bioperl 1.5 that has been fixed in the latest
> release.  Get the new release (bioperl-1.5.1-rc3.tar.gz) here:
> http://bioperl.org/DIST and upgrade.
>
> Barry
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Sam
> Al-Droubi
> Sent: Saturday, October 15, 2005 8:54 PM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] bioperl genbank output is different than web?
>
> All,
>
> I am new to this so please forgive me for any dump
> quetsions.
>
> The problem: I am getting the genbank data for a gene
> using the simple code below and writing it to a file.
> The problem is that output is not the same as when I
> do a web search via ncbi entrez.  I want to parse out
> on which chromosome gene is on.  The web output gives
> me a correct chromosome number (i.e. chromosome="3")
> while the output from this code gives me (i.e.
> /chromosome="Bio::Annotation::SimpleValue=HASH(0x88be668)")
>
> Can someone help me figure out what is wrong please?
>
> The Code:
> --------------------
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> use Bio::Seq;
>
> $db_obj = Bio::DB::GenBank->new;
> $seq_obj = $db_obj->get_Seq_by_acc("NM_011674");
> $seqio_obj = Bio::SeqIO->new(-file
> =>">data/genes/NM_011674.fa", -format=>"fasta");
> $seqio_obj = Bio::SeqIO->new(-file
> =>">data/genes/NM_011674.gb", -format=>"genbank");
> $seqio_obj->write_seq($seq_obj);
> ---------------------
>
>
>
>
>
>
> Sincerely,
> Sam Al-Droubi, M.S.
> saldroubi at yahoo.com
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12