[Bioperl-l] Local database building
Fri, 05 Oct 2001 10:00:12 -0700
Aha... I new this should have been familiar. So this seems like a really
nice implementation, and for starters I just threw these two scripts from
the tutorial (one to index, the other to retrieve) at bioperl using a faux
file to be indexed (the index script is index.pl, the retrieve script is
>index.pl PEP pep.fas
[where pep.fas has:
this created PEP.pag and PEP.dir
then, after adding a print $seq line to the retrieve script:
>perl fetch.pl PEP 123
What did I miss? Also is there a simple way to verify that the index files
(the .pag and .dir) have been created correctly?
Thanks for the help :).
----- Original Message -----
From: "Heikki Lehvaslaiho" <firstname.lastname@example.org>
To: "Jason Raymond" <email@example.com>
Sent: Friday, October 05, 2001 1:15 AM
Subject: Re: [Bioperl-l] Local database building
> This should be an easy thing. You can use either Bio::Index::Fasta which
> uses dbm or you can get bioperl-db from the CVS repository which does the
> same thing with mySQL as a back end.
> Try Bio::Index::Fasta first. You'll find an introduction to it in
> bptutorial.pl section III.1.2.
> Jason Raymond wrote:
> > Another newbie question for the group :). I'm trying to setup a local
> > database from several sets of Fasta-formatted genomes, and I'm hoping to
> > a rough step-by-step on how to do this (or where to read more on this).
> > Most of this data is in the format:
> > >orf1@contig16@8@8 35 745 Predicted orf
> > LDSIFLEF....
> > >orf3@contig21@8@12 35 431 Predicted orf
> > MEITAL....
> > ...
> > would this be something that can be 'smoothly' built into a database so
> > I can later retrieve sequences with Perl scripts? Also, as of right now
> > have about 10 different files in this format, and I would ideally like
> > all to be in one single database. Is this feasible?
> > Thanks again!
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperlfirstname.lastname@example.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
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