[Bioperl-l] how to parse the GenPept sequence object to get the'DBSOURCE' field

[Brian Osborne]

Hilmar,

Excellent. OK, I need some suggestions as to values, this is an annotation
that I've never constructed. Here's an example:

DATABASE GenBank

PRIMARY_ID AAC12345

OPTIONAL_ID AAC12345.2

COMMENT: ?

TAGNAME: dblink

NAMESPACE: ?

AUTHORITY: ?

VERSION: 2


Brian O.


-----Original Message-----
From: Hilmar Lapp [mailto:hlapp at gmx.net]
Sent: Thursday, March 17, 2005 7:18 PM
To: Brian Osborne
Cc: Leonardo Kenji Shikida; bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] how to parse the GenPept sequence object to get
the'DBSOURCE' field


Isn't this a dbxref? So, yes the work should be in genbank.pm but it
should create a Bio::Annotation::DBLink object instead of a
SimpleValue. DBLink will also properly represent version, accession,
and database, instead of just a flat string.

	-hilmar

On Thursday, March 17, 2005, at 06:06  AM, Brian Osborne wrote:

> K,
>
> I've added some code to SeqIO/genbank.pm that appears to work but I
> can't
> commit it until I ask the Bioperl designers a question. Namely, it
> appears
> that this DBSOURCE field is specific to Genbank Protein, so the work of
> creating the Annotation::SimpleValue should be in genbank.pm, not
> RichSeq.pm, right?
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Leonardo
> Kenji Shikida
> Sent: Wednesday, March 16, 2005 2:16 PM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] how to parse the GenPept sequence object to get
> the'DBSOURCE' field
>
>
> does anyone know how to parse the GenPept sequence object to get the
> 'DBSOURCE' field?
>
> e.g. human.protein.gpff
>
> LOCUS       NP_000358                245 aa            linear   PRI
> 31-OCT-2000
> DEFINITION  thiopurine S-methyltransferase [Homo sapiens].
> ACCESSION   NP_000358
> VERSION     NP_000358.1  GI:4507653
> DBSOURCE    REFSEQ: accession NM_000367.1  <<==
> KEYWORDS    .
> SOURCE      Homo sapiens (human)
>
> I found no answer reading the docs, and there is the same unanswered
> question in this list archives at
>
> http://bioperl.org/pipermail/bioperl-l/2003-June/012438.html
>
> thanks in advance
>
> K.
>
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--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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