[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1168 (fwd)

[Jason Stajich]

There is no currently accepted format in the GenBank/EMBL feature tables
for writing anything other than what we consider 'generic' features.  If
you have an idea on what would be an appropriate way to represent them in
genbank/embl FT format we'd love to hear it and we could work with you on
implementing it.  It was never done because no one has really seen a
"right way" to deal with them in this format.

How would you suggest writing a feature pair or a SeqFeature::Computation
object that fits into the official format:
http://www.ncbi.nlm.nih.gov/collab/FT/index.html

No one has volunteered recently to work on dealing with these features in
genbank/embl formats - Would you be willing to work on it?

This is how things get done in the open-source world - if it doesn't work
or exist yet, you propose a solution to get feedback and then you write it
and everyone benefits.

-jason
---
Jason Stajich
Duke University
jason@cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Fri, 19 Apr 2002 17:04:33 -0400
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1168

JitterBug notification

new message incoming/1168

Message summary for PR#1168
	From: mingyi.liu@gpc-biotech.com
	Subject: Lack of features in genbank.pm/FTHelper
	Date: Fri, 19 Apr 2002 17:04:32 -0400
	0 replies 	0 followups

====> ORIGINAL MESSAGE FOLLOWS <====

>From mingyi.liu@gpc-biotech.com Fri Apr 19 17:04:33 2002
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Date: Fri, 19 Apr 2002 17:04:32 -0400
Message-Id: <200204192104.g3JL4WkO030392@pw600a.bioperl.org>
From: mingyi.liu@gpc-biotech.com
To: bioperl-bugs@bioperl.org
Subject: Lack of features in genbank.pm/FTHelper

Full_Name: Mingyi Liu
Module: Bio::SeqIO::genbank, Bio::SeqIO::FTHelper
Version: 1.0
PerlVer: 5.6.1
OS: Win2K
Submission from: cambridge.gpc-biotech.com (63.74.162.108)


V1.0 improved upon 0.7 by adding support for Computation, FeaturePair etc.
modules, but when genbank writes features out, these features do not actually
write all contents out.  Is that a bug or it's just that it's not actually
implemented yet?  I didn't find any code supporting writing info for those newly
added modules.  Seems only generic features got written.  Is there any time line
on when these features will be implemented?


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