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.IX Title "BP_BIOFLAT_INDEX 1p"
.TH BP_BIOFLAT_INDEX 1p "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
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.SH "NAME"
bp_bioflat_index.pl \- index sequence files using Bio::DB::Flat
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 3
\& 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.
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.SH "USAGE"
.IX Header "USAGE"
.Vb 1
\& 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".
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.PP
Options can be abbreviated.  For example, use \-i for \-\-indextype.
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The following environment variables will be used as defaults if the 
corresponding options are not provided:
.PP
.Vb 4
\&     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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