Provided by: bioperl_1.6.924-3_all bug

NAME - indexes files for use by

SYNOPSIS index_name file1 file2 etc.

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

 nrdb /data/nrdb/nrdb.fasta

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

 -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 built 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 bp_fetch which fetches sequences and pipes them to STDOUT, for

          bp_fetch swiss:ROA1_HUMAN

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


         -fmt  <format>   - Fasta (default), swiss or EMBL
         -dir  <dir>      - directory where the index files are found
                            (overrides BIOPERL_INDEX environment variable)

       Options for expert use

         -type <db_type>  - DBM_file type.
                            (overrides BIOPERL_INDEX_TYPE environment variable)
         -v               - report every index addition (debugging)


       bp_index and bp_fetch coordinate where the databases lie using the enviroment variable
       BIOPERL_INDEX. This can be overridden using the -dir option. There is no default value, so
       you must use the -dir option or set BIOPERL_INDEX.

       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 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 bp_fetch code).


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


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AUTHOR - Ewan Birney

       Ewan Birney <>