[Bioperl-l] formatdb

Phil Princely phil.princely at gmail.com
Fri Sep 8 01:53:31 EDT 2006


hi all

I'm new to this list, and new to BioPerl, so excuse me if this is off topic.

My background is computers, but I'm working with BLAST at the moment.
I've installed BLAST and have it running nicely on MacOS X. I found
that entering a new database for use in WWWBLAST was tedious, with 5
or so steps, so I wrote a perl script which does the following:

takes the input of a FASTA file name, and n or p, if it's a nucleotide
of protein sequence
runs it through formatdb, with the correct flags
moves the output files to the correct directory
changes the config and html files so that the new database is
accessible in WWWBLAST

My script isn't the prettiest, or the most error resistant. Then I
found BioPerl and was wondering if the same functionality is built in.
So my question is..

Is there an easy way to run formatdb and change the relevant files
using BioPerl?

Sorry if this is off topic, and thanks in advance

Phil P.


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