[Bioperl-l] Entrezgene parser: new parser available
from sourceforge (attached too) (fwd)
skirov at utk.edu
Mon Apr 18 14:02:18 EDT 2005
OK. Makes sense.
Hilmar Lapp wrote:
> I'd rather put it into its own test just to keep things easier for
> now. Once the parser and API has settled it can still be appended to
> the SeqIO.t.
> On Monday, April 18, 2005, at 05:46 AM, 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
>> 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
>> low level parser. Anyone who uses his parser direcly will have to
>> 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!
>> 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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