This is the command bp_bioflat_indexp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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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