[Bioperl-l] Parsing FASTA m10 output

Chris Fields cjfields at uiuc.edu
Tue Apr 17 12:49:53 EDT 2007


You can post here or add it to Bugzilla as an enhancement request if  
the code is particularly long.

chris

On Apr 17, 2007, at 11:21 AM, Ioannis Kirmitzoglou wrote:

> Thanks for the prompt reply...
> Seems like I will have to "quit talking and begin doing"
> I will post the code here in case someone else finds himself in the  
> same
> situation...
>
> -- 
> Ioannis Kirmitzoglou, MSc
> PhD. Student,
> Bioinformatics Research Laboratory
> Department of Biological Sciences
> University of Cyprus
>
>
> On 17/04/07, Thiago Venancio < thiago.venancio at gmail.com> wrote:
>> I am parsing FASTA outputs these days.
>>
>> The m 10 format is a recent implementation, not so popular yet.  
>> So, I have
>
>> first tested the Bio::SearchIO against a default output and  
>> everything is
>> fine.
>>
>> I think future releases of Bio::SearchIO will deal with the m10  
>> output. By
>> now, you can run all again or code a little bit to parse what you  
>> want
> (not
>> a hard task).
>>
>> T.
>>
>>
>> On 4/17/07, Ioannis Kirmitzoglou < IoannisKirmitzoglou at gmail.com>  
>> wrote:
>>>
>>> I apologize if this question has already been answered but my search
> came
>> up
>>> with no relevant results.
>>> I am new to the FASTA program and after reading the fasta3x.doc I
> decided
>> to
>>> run it using the m10 output. The reason for doing such a choice was
>>>
>>> Quote from fasta3x.doc:
>>>      -m 10 is a new, parseable format for use with other
>>>      programs....
>>>
>>>
>>> I ran FASTA in batch mode and waited about 3-4 days for the results.
>>> My problem is that today, when i started writing a perl script to  
>>> parse
>> the
>>> output I realized that SearchIO doesn't supports m10 format.
>>> Seems like I had to be more careful...
>>> Before starting coding a module that will be able to parse the  
>>> output
> (or
>>> re-running FASTA with -m9 -d0 switches which will take 4 more  
>>> days) I
>> would
>>> be really thankful if any of you knows of any other way to parse  
>>> those
>>> files?
>>> Thanks in advance...
>>>
>>> Ioannis Kirmitzoglou, MSc
>>> PhD. Student,
>>> Bioinformatics Research Laboratory
>>> Department of Biological Sciences
>>> University of Cyprus
>>>
>>> --
>>> View this message in context:
>> http://www.nabble.com/Parsing-FASTA-m10-output- 
>> tf3590568.html#a10034698
>>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
>> --
>> "The way to get started is to quit talking and begin doing."
>>       Walt Disney
>>
>> ========================
>> Thiago Motta Venancio, MSc
>> PhD student in Bioinformatics
>> University of Sao Paulo
>> ========================
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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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