[Bioperl-l] Entrezgene parser: new parser available
from sourceforge (attached too) (fwd)
skirov at utk.edu
Mon Apr 18 10:47:44 EDT 2005
I will put the tests, but I am a bit busy this week. I will try to do it
on Friday or during the weekend.
Brian Osborne wrote:
>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
>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
>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)
>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!
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
tel +865 576 5120
e-mail: skirov at utk.edu
sao at ornl.gov
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For the love of God and our human rights
And all these things are swept aside"
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