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

[Hilmar Lapp]

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.

	-hilmar

On Monday, April 18, 2005, at 05:46  AM, Brian Osborne wrote:

> Stefan,
>
> 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
> Kirov
> 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.
> Stefan
>
> ---------- 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!
>
> Mingyi
>
>
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>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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