[Bioperl-l] PAML parser failed for PAML 4.3b and 4.1

[Mark A. Jensen]

Yong-- say 'ni hao' to Manyuan for me --- cheers MAJ
----- Original Message ----- 
From: "pkuonline" <pkuonline at gmail.com>
To: "Chris Fields" <cjfields at illinois.edu>
Cc: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Wednesday, December 23, 2009 5:45 PM
Subject: Re: [Bioperl-l] PAML parser failed for PAML 4.3b and 4.1


> Hi Chris,
>
> Thanks for your reply and I just submitted this bug to bugzilla.
>
> Have a nice holiday!
> -------------------------------------------------------------
> Yong Zhang
> Ph.D, Research Scholar
> Manyuan Long's Lab
> University of Chicago
>
>>-------------------------------------------------------------
>>From: Chris Fields
>>Time: 2009-12-23 15:19:50
>>To: pkuonline  bioperl-l
>>Subject: Re: [Bioperl-l] PAML parser failed for PAML 4.3b and 4.1
>
>>Well, not completely unexpected, but very frustrating nonetheless.  Changes to 
>>PAML output have broken in just about every PAML parser revision.  Not sure 
>>when this will be addressed unfortunately, my hope is sooner than later.
>>
>>Can you file a bioperl bug report for this?  It's the best place to keep 
>>track.
>>
>>http://bugzilla.open-bio.org/
>>
>>chris
>>
>>On Dec 23, 2009, at 12:36 PM, pkuonline wrote:
>>
>>> Hi Everyone,
>>>
>>> I used the latest Bioperl build, 
>>> http://www.bioperl.org/DIST/nightly_builds/bioperl-live.tar.gz and tried to 
>>> parse CODEML result. I searched the mail list and found current PAML parser 
>>> is compatible with PAML 4.3a, 
>>> http://lists.open-bio.org/pipermail/bioperl-l/2009-November/031602.html. 
>>> However, recently, Ziheng Yang updates his PAML to 4.3b. I found the parser 
>>> does not work. More strangely, I tested it on the old PAML 4.1 result and 
>>> also failed.
>>>
>>> I attached my CODEML outputs here to see whether you guys have some idea.
>>>
>>> Many thanks ahead!
>>>
>>> Best regards,
>>> -------------------------------------------------------------
>>> Yong Zhang
>>> Ph.D, Research Scholar
>>> Manyuan Long's Lab
>>> University of 
>>> Chicago<rst4.1><mlc4.1><mlc4.3b><rst4.3b>_______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>


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