[Bioperl-l] parsing of codeml

Chris Fields cjfields at uiuc.edu
Tue Jul 15 09:01:22 EDT 2008


I agree, the mailing list is the place to ask.  However, it would be  
best to add the files as a bug report in bugzilla.

Mailing list info:

http://www.bioperl.org/wiki/Mailing_lists

bioperl-l at lists.open-bio.org

chris

On Jul 15, 2008, at 12:25 AM, Jason Stajich wrote:

> Are you really sure you want to use runmode=2 ? we have never really  
> tested or tried to support that combination.
> It is much better to just provide your own tree - Yang talks about  
> this in the handbook that PAML is not a good tree building program.
>
> I would still encourage you to submit this as bug to bugzilla with  
> the files you sent me.
> Honestly, I don't really know when I'll have much time to look into  
> this. I'll try but no promises.  I really encourage you to use the  
> mailing list to see if you can get help from other developers as well.
>
> -jason
>
> On Jul 9, 2008, at 6:23 PM, Tannistha wrote:
>
>> Hi Jason,
>>
>> Hope you have received my earlier email having input file and  
>> results.  Please let me know if I  am to provide with any further  
>> information.
>>
>> Thanking you
>>
>> Best  Regards
>> Tannistha
>>
>> Dr. Tannistha Nandi   email: tannistha3 at yahoo.com
>>
>> --- On Thu, 7/3/08, Jason Stajich <jason at bioperl.org> wrote:
>> From: Jason Stajich <jason at bioperl.org>
>> Subject: Re: parsing of codeml
>> To: "Tannistha" <tannistha3 at yahoo.com>
>> Date: Thursday, July 3, 2008, 8:54 PM
>>
>> It is more useful to also send the data and/or codeml report file so
>> I can actually duplicate the parsing problem directly.
>> Best scenario is to submit it as a bug to the bugzilla as well  
>> http://
>> bugzilla.open-bio.org/
>>
>> I'm still on the road @ another conference but if you can send the
>> data I'll take a look at debugging when I have a free moment.
>>
>> thanks for your patience.
>> -jason
>> On Jul 3, 2008, at 12:45 AM, Tannistha wrote:
>>
>>> Hi Jason,
>>>
>>> I think I am able to narrow down my problem. Now the issue is when
>>> I use runmode =2, seqtype =1, and Mgene =1 for a set of 8 genes
>>> (multiple sequence alignment), it is not able to parse the result
>>> generated by codeml.
>>> I sending the runPAML.pl script I am using. Apart from this I am
>>> using the SVN code of PAML.pm and codeml.pm. I am running on  red
>>> hat linux using Bioperl 1.5.2 and PAML4.
>>> I will be grateful if you could spare some time of yours to look
>>> into my problem.
>>>
>>> Thanking you
>>>
>>> Best Regards
>>> Tannistha
>>>
>>>
>>> Dr. Tannistha Nandi
>>> email: tannistha3 at yahoo.com
>>>
>>> --- On Wed, 6/25/08, Jason Stajich <jason at bioperl.org> wrote:
>>>
>>> From: Jason Stajich <jason at bioperl.org>
>>> Subject: Re: Please take a look in this issue
>>> To: tannistha3 at yahoo.com
>>> Date: Wednesday, June 25, 2008, 1:18 PM
>>>
>>>
>>> i'm sorry, i'm away for the next 2 weeks, I'm not sure when I
>> can
>>> look into your issue. I would ask the list again if you don't get a
>>> response in a few days or try and also use the code from SVN  
>>> directly.
>>>
>>>
>>> On 6/25/08, Tannistha <tannistha3 at yahoo.com> wrote:
>>> Hi Jason
>>>
>>> I have posted my query in the forum, but no luck yet.
>>>
>>> I am using your new PAML script updated 4 days back, but its giving
>>> error in these line in PAML.pm
>>> --------------------------
>>> return unless (/^Nei\s*\&\s*Gojobori/);
>>>    # skip the next line is ver > 3.15
>>>    $self->_readline if ($ver > 3.14);
>>> ------------------------------------------------
>>>
>>> Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/
>>> site_perl/5.8.5/Bio/Tools/Phylo/PAML.pm line 745, <GEN2> line 90.
>>>
>>> Please help me to fix this. I am using Bioperl 1.5.2 and PAML4
>>>
>>> Thanking you
>>>
>>> Regards
>>> Tannistha
>>>
>>>
>>> Dr. Tannistha Nandi
>>> email: tannistha3 at yahoo.com
>>>
>>> --- On Mon, 6/23/08, Jason Stajich <jason at bioperl.org> wrote:
>>>
>>> From: Jason Stajich <jason at bioperl.org>
>>> Subject: Fwd: PAML through BIOPERL - parsing error
>>> To: tannistha3 at yahoo.com
>>> Cc: "bioperl list" <bioperl-l at lists.open-bio.org>
>>> Date: Monday, June 23, 2008, 11:02 PM
>>>
>>>
>>> You'll have to report what version of BioPerl and PAML you are
>>> using, only certain versions work together because the report
>>> output from PAML changes in each version.  We have tried to fix it
>>> for PAML4 in the latest code in SVN and I believe PAML 3.15 should
>>> work with what is in 1.5.2 release of BioPerl  but I'm not sure.
>>>
>>>
>>> Please direct your questions to the mailing list to insure someone
>>> has a chance to look at it.
>>>
>>>
>>>
>>> -jason
>>>
>>>
>>>
>>>
>>> Begin forwarded message:
>>>
>>>
>>> From: Tannistha <tannistha3 at yahoo.com>
>>> Date: June 22, 2008 10:43:41 PM PDT
>>> To: jason at bioperl.org
>>> Subject: PAML through BIOPERL - parsing error
>>> Reply-To: tannistha3 at yahoo.com
>>>
>>>
>>>
>>>
>>> Hi Jason,
>>>
>>> I am using PAML through BIOPERL. My input in multiple CDS sequence.
>>> I am getting an error while parsing my codeml result.
>>> The error is:
>>> Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/
>>> site_perl/5.8.5/Bio/Tools/Phylo/PAML.pm line 615, <GEN2> line 90.
>>>
>>>
>>> Please suggest how to eliminate this error.
>>>
>>> Thanking you
>>>
>>> Regards
>>>
>>>
>>> Dr. Tannistha Nandi
>>> email: tannistha3 at yahoo.com
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -- 
>>> Jason Stajich
>>> jason at bioperl.org
>>> http://bioperl.org/wiki/User:Jason
>>>
>>>
>>> <runPaml.pl>
>>
>>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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