/ 
bioperl-0.7.0
/ bpindex.pl

NAME

bpindex.pl - indexes files for use by bpfetch

SYNOPSIS

bpindex.pl index_name file1 file2 etc

DESCRIPTION

bpindex.pl builds a bioperl index for the sequence files given in the argument list, under the index name. For example

bpindex.pl nrdb /data/nrdb/nrdb.fasta

would build an index called 'nrdb' as the index name for the file nrdb.fasta, and

bpindex.pl -fmt EMBL swiss /data/swiss/*.dat

would build an index called swiss for all the files in /data/swiss which end in .dat which are in EMBL format.

The indexes are build using the Bio/Index/* modules, in particular, Bio::Index::EMBL and the Bio::Index::Fasta modules. Any script which uses these modules can use the index. A good example script is bpfetch which fetches sequences and pipes them to stdout, for example

bpfetch swiss:ROA1_HUMAN

gets the ROA1_HUMAN sequence from the swiss index and writes it as fasta format on stdout

OPTIONS

-fmt  <format>   - Fasta (default), swiss or EMBL
-v               - report every index addition (debugging)

options only for expert use

-dir  <dir>      - directory to find the index files
                   (overrides BIOPERL_INDEX environment varaible)
-type <db_type>  - DBM_file type. 
                   (overrides BIOPERL_INDEX_TYPE environment varaible)

ENVIRONMENT

bpindex and bpfetch coordinate where the databases lie using the enviroment variable BIOPERL_INDEX. This can be overridden using the -dir option.

The DB type is coordinated with BIOPERL_INDEX_TYPE which if it is not there, defaults to whatever the bioperl modules have installed, which itself defaults to SDBM_File.

USING IT YOURSELF

bpindex.pl is a script that drives the Index modules. If you want to use this script heavily in your work, if it is Perl based, it is almost certainly better to look at the code in this script and copy it across (probably you will be more likely to want to use the bpfetch code).

EXTENDING IT

bpindex is just a wrapper around James Gilbert's excellent Index modules found in bioperl

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
http://bio.perl.org/MailList.html             - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bio.perl.org                   
http://bio.perl.org/bioperl-bugs/

AUTHOR

Ewan Birney, birney@sanger.ac.uk