building flat files in unix and importing them from windows Post: 54156

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LEARN ABOUT DEBIAN

bp_bioflat_index

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

NAME

       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

	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 v5.14.2							    2012-03-02						      BP_BIOFLAT_INDEX(1p)