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

[Brian Osborne]

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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