[Bioperl-l] A question about iBio::Index: and its correct use

Mark A. Jensen maj at fortinbras.us
Thu Nov 5 10:39:05 EST 2009


José -- It looks like this is a good solution to your problem. Please send you 
script so we can look at it-
cheers Mark
----- Original Message ----- 
From: <jluis.lavin at unavarra.es>
To: <bioperl-l at lists.open-bio.org>
Sent: Thursday, November 05, 2009 10:28 AM
Subject: [Bioperl-l] A question about iBio::Index: and its correct use



Hello to all,

I´m trying to write a script to retrieve a list of sequences from a local
FASTA file (for example a fasta archive where all the protein models of an
organism are stored). This file would be used by me as some kind "local
database" (sorry if I mistake a few concepts...)
I´ve been reading the BioPerl HOWTOs and I came across the
Bio::Index::Fasta tool.
If I didn´t misunderstood what I read (which can be easy because my low
level on programming) this Indexing tool should do the job.
I wrote a couple of scripts based on the documentation i read about this
tool, but I don´t seem to be able to create the index file to be used
later (to retrieve the sequences from).
-First of all, I want to ask the people in this forum if the
Bio::Index::Fasta is the right one to chose for this tasks.
-Then I´ll beg you to take a look at my scripts, because I don´t seem to
catch the bug...

Best wishes to you all and thanks in advance ;)

-- 
José Luis Lavín Trueba, PhD

Dpto. de Producción Agraria
Grupo de Genética y Microbiología
Universidad Pública de Navarra
31006 Pamplona
Navarra
SPAIN


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