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.
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