Christopher Fields > BioPerl-1.6.920 > bp_bioflat_index.pl

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NAME ^

bp_bioflat_index.pl - index sequence files using Bio::DB::Flat

DESCRIPTION ^

 Create or update a biological sequence database indexed with the
 Bio::DB::Flat indexing scheme.  The arguments are a list of flat files
 containing the sequence information to be indexed.

USAGE ^

 bp_bioflat_index.pl <options> file1 file2 file3...

 Options:

     --create              Create or reinitialize the index.  If not specified,
                           the index must already exist.

     --format   <format>   The format of the sequence files.  Must be one
                           of "genbank", "swissprot", "embl" or "fasta".

     --location <path>     Path to the directory in which the index files
                           are stored.

     --dbname <name>       The symbolic name of the database to be created.

     --indextype <type>    Type of index to create.  Either "bdb" or "flat".
                           "binarysearch" is the same as "flat".

Options can be abbreviated. For example, use -i for --indextype.

The following environment variables will be used as defaults if the corresponding options are not provided:

     OBDA_FORMAT      format of sequence file
     OBDA_LOCATION    path to directory in which index files are stored
     OBDA_DBNAME      name of database
     OBDA_INDEX       type of index to create
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