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

6       bioflat_index.pl - index sequence files using Bio::DB::Flat
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DESCRIPTION

9        Create or update a biological sequence database indexed with the
10        Bio::DB::Flat indexing scheme.  The arguments are a list of flat files
11        containing the sequence information to be indexed.
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USAGE

14        bioflat_index.pl <options> file1 file2 file3...
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16        Options:
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18            --create              Create or reinitialize the index.  If not specified,
19                                  the index must already exist.
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21            --format   <format>   The format of the sequence files.  Must be one
22                                  of "genbank", "swissprot", "embl" or "fasta".
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24            --location <path>     Path to the directory in which the index files
25                                  are stored.
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27            --dbname <name>       The symbolic name of the database to be created.
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29            --indextype <type>    Type of index to create.  Either "bdb" or "flat".
30                                  "binarysearch" is the same as "flat".
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32       Options can be abbreviated.  For example, use -i for --indextype.
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34       The following environment variables will be used as defaults if the
35       corresponding options are not provided:
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37            OBDA_FORMAT      format of sequence file
38            OBDA_LOCATION    path to directory in which index files are stored
39            OBDA_DBNAME      name of database
40            OBDA_INDEX       type of index to create
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44perl v5.8.8                       2007-05-07               BP_BIOFLAT_INDEX(1)
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