[Bioperl-l] Parsing FASTA m10 output
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.
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
> 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
>> 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
>> a hard task).
>> On 4/17/07, Ioannis Kirmitzoglou < IoannisKirmitzoglou at gmail.com>
>>> I apologize if this question has already been answered but my search
>>> with no relevant results.
>>> I am new to the FASTA program and after reading the fasta3x.doc I
>>> 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
>>> 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
>>> 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
>>> re-running FASTA with -m9 -d0 switches which will take 4 more
>>> days) I
>>> be really thankful if any of you knows of any other way to parse
>>> Thanks in advance...
>>> Ioannis Kirmitzoglou, MSc
>>> PhD. Student,
>>> Bioinformatics Research Laboratory
>>> Department of Biological Sciences
>>> University of Cyprus
>>> View this message in context:
>>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> "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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