[Bioperl-l] Genbank LOCUS entry

Brian Osborne brian_osborne at cognia.com
Wed Feb 2 18:46:28 EST 2005


You will write the Genbank entry to a string, using the Seq object
(http://bioperl.org/Core/Latest/faq.html#Q2.4), and use a regular

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 Matthias
Sent: Wednesday, February 02, 2005 5:30 PM
To: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Genbank LOCUS entry

On Wed, Feb 02, 2005 at 01:52:01PM -0800, Hilmar Lapp wrote:
> You do get the LOCUS name - what you are asking for is the entire LOCUS
> line. There no method for the entire line; but if that's all you need
"The id is equivalent to the LOCUS field of the GenBank/EMBL databanks"
(from http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html,
description of the display_id method)

> 	$ grep "^LOCUS" < my-genbank-file
> on the command line.
As shown in the little example skript the Perl::Seq object is obtained
from the ncbi database, there is no my-genbank-file. Your solution is a
workaround. It's looks a little ugly to me to save it into a genbank file
an grep the LOCUS line, back to the same perl script...


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