[Bioperl-l] new modules for sarching for patterns in fasta-fi les

Amir Karger akarger at CGR.Harvard.edu
Tue Aug 16 08:17:19 EDT 2005

> -----Original Message-----
> From: Heikki Lehvaslaiho [mailto:heikki at ebi.ac.uk] 
> On Tuesday 09 August 2005 20:20, Amir Karger wrote:
> >
> > I wrote a simple one-liner to convert fasta to three, tab-separated
> > columns: ID (without '>') desc, and concatenated sequence. 
> FYI, this is  already implemented as 'tab' format in Bio::SeqIO.
>  -Heikki

I decided to write a separate translator for two reasons. First, I thought
people might want the desc in a separate column. (SeqIO::tab just takes the
entire desc line in one shot, right?) Second, I believe that some people who
use the Scriptome toolbox might not have Bioperl installed, and I don't want
to force them to have Bioperl just to parse some FASTAs. (OTOH, I was Lazy
enough to steal Bio::SeqIO to do most format conversions.)  


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