[Bioperl-l] Tandem Repeats finder parser

Chris Fields cjfields at uiuc.edu
Tue Mar 13 11:27:27 EDT 2007


Sounds fine by me.  As for the versioning issue you can always state  
the minimal version supported in POD.

chris

On Mar 13, 2007, at 9:37 AM, Eric Just wrote:

> Hi Stefan
>
> Trf does indeed store the parameters in the filename, however it also
> has a parameters line in the output file which is where I pull the
> parameters from:
>
> Parameters: 2 7 7 80 10 50 12
>
> That may be a new feature, I'm using Tandem Repeats Rinder version
> 4.00   I was planning on using that since the file name is not
> necessarily stable (a user can rename the file).  Sound reasonable?
>
> Eric
>
>
> On 3/13/07, Stefan Kirov <stefan.kirov at bms.com> wrote:
>> Eric,
>> The last time I used it, trf had a funny way of assigning  
>> filenames. Do
>> you plan to parse the filenames and extract the parameters from  
>> there,
>> or you are going to stick only to the content?
>> If you can parse the filenames, that might be very useful.
>> Stefan
>>
>> Chris Fields wrote:
>>> I don't see a problem.  The best place for it is prob. in the
>>> Bio::Tools namespace (unless you have other ideas).
>>>
>>> chris
>>>
>>> On Mar 12, 2007, at 5:02 PM, Eric Just wrote:
>>>
>>>
>>>> Hi there,
>>>>
>>>> I have written a simple parser for Tandem Repeats Finder  
>>>> output.   Is
>>>> there any interest in including this module in Bioperl?  If so,  
>>>> I will
>>>> conform it to Bioperl standards, write some tests, then send it to
>>>> whomever is interested.
>>>>
>>>> Eric
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
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>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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