[Bioperl-l] Parsing FASTA m10 output
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
Ioannis Kirmitzoglou, MSc
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 want
> a hard task).
> On 4/17/07, Ioannis Kirmitzoglou < IoannisKirmitzoglou at gmail.com> wrote:
> > 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
> > 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
> > 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
> > 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 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:
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
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> "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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