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BP_BIOFLAT_INDEX(1)   User Contributed Perl Documentation  BP_BIOFLAT_INDEX(1)

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

perl v5.20.2                      2015-09-15               BP_BIOFLAT_INDEX(1)