05-10-2011
This is too complex to consider without some detailed knowledge of the record structure and what you are trying to achieve. Trying to create a relational database using flat files and shell script is asking for trouble. Really needs a Systems Analyst.
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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)