[Bioperl-l] Parsing FASTA m10 output

Ioannis Kirmitzoglou ioanniskirmitzoglou at gmail.com
Tue Apr 17 12:21:36 EDT 2007


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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