1BP_BIOFLAT_INDEX(1) User Contributed Perl Documentation BP_BIOFLAT_INDEX(1)
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6 bioflat_index.pl - index sequence files using Bio::DB::Flat
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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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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
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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)