[Bioperl-l] Entrezgene parser: new parser available from sourceforge (attached too) (fwd)

Brian Osborne brian_osborne at cognia.com
Mon Apr 18 08:46:37 EDT 2005


Unless I've missed something it seems that someone needs to add a test for
this new parser, the best place would be t/SeqIO.t. Could you add a
mini-Entrez Gene file to t/data as a first step? I'm assuming that such a
thing exists...

Thanks again,

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 Stefan A
Sent: Tuesday, April 05, 2005 3:07 PM
To: Bioperl
Subject: [Bioperl-l] Entrezgene parser: new parser available from
sourceforge (attached too) (fwd)

As often happens, NCBI introduced some small, but interesting changes to
their ASN entrezgene format. Therefore Mingyi had to change the underlying
low level parser. Anyone who uses his parser direcly will have to update.
This will also delay the release of the first version of the bioperl
entrezgene parser, which I anticipated to be on Thursday. I still hope I
will commit the code on Friday.

---------- Forwarded message ----------
Date: Tue, 05 Apr 2005 13:35:57 -0400
From: Mingyi Liu <mingyi.liu at gpc-biotech.com>
To: Stefan A Kirov <skirov at utk.edu>
Subject: new parser available from sourceforge (attached too)

Hi, Stefan,

I attached the new version to this email.  Unfortunately as expected,
the new version is much slower due to the use of lookahead regexes
(needed to accomodate the meaningless/buggy changes NCBI introduced).
About 30% slower in my test.  Still can't find a good reason why they
introduced those 3 different types of changes.  Can't be one bug.

Anyways.  Thanks for letting me know so early!


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