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