[Bioperl-l] trouble parsing swissprot annotations

[Brian Osborne]

Antonio,

> the aminoacid substituted. This info is not contained neither in the tags
nor as subfeatures.

Most of the data in a Swissprot file is contained in Annotation objects, and
those objects are contained within an AnnotationCollection object. Did you
look there? The Feature-Annotation HOWTO talks about this, though not always
with Swissprot in mind.

>$feato_bj->display_name doesn't print anything (gives an

This doesn't sound good. Can you submit this to http://bugzilla.bioperl.org/
and attach a Swissprot file that will demonstrate this?

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 Antonio Ramos
Fernández
Sent: Friday, May 21, 2004 3:06 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] trouble parsing swissprot annotations

Hello, I have tried to parse annotations from a local copy of swissprot
using Bio::SeqIO ($seq->get_SeqFeatures). I am interested in aminoacid
prostranslational modifications, conflicts an variants.
I can extract primary tags (TRANSMEM, HELIX...) and locations ( start, end),
but I cannot extract the string containing the name of the modification or
the aminoacid substituted. This info is not contained neither in the tags
nor as subfeatures. $feato_bj->display_name doesn't print anything (gives an
error 'use of initialized value in print or ...').

How can I extract, for example 'MOD_RES 117 117 Phosphoserine' or 'CONFLICT
232   232           G -> S ' withour having to build a new parser? (that is,
I can't get the 'phosphoserine', which one is the right method?)

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