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bp_bioflat_index.pl
Langue: en
Version: 2009-02-27 (fedora - 04/07/09)
Section: 1 (Commandes utilisateur)
Sommaire
NAME
bioflat_index.pl - index sequence files using Bio::DB::FlatDESCRIPTION
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
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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