[Bioperl-l] Local database building

[Jason Raymond]

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
fetch.pl):

>index.pl PEP pep.fas

[where pep.fas has:
>123
AAAAAA
>124
ASASAS
>125
SSSSSS
]
this created PEP.pag and PEP.dir

then, after adding a print $seq line to the retrieve script:
>perl fetch.pl PEP 123
outputs:
Bio::Seq=HASH(0x1eb51ec)

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" <heikki@ebi.ac.uk>
To: "Jason Raymond" <jasonraymond@asu.edu>
Cc: <bioperl-l@bioperl.org>
Sent: Friday, October 05, 2001 1:15 AM
Subject: Re: [Bioperl-l] Local database building


> Jason,
>
> 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.
>
> -Heikki
>
> 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
get
> > 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
that
> > I can later retrieve sequences with Perl scripts?  Also, as of right now
I
> > have about 10 different files in this format, and I would ideally like
them
> > all to be in one single database.  Is this feasible?
> > Thanks again!
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
>
> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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