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


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.


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


--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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