NAME

       bp_seqfeature_load.pl - Load GFF into a SeqFeature database

DESCRIPTION

       Pass any number of GFF or fasta format files (or GFF with embedded fasta) to load the features and
       sequences into a SeqFeature database. The database (and adaptor) to use is specified on the command line.
       Use the --create flag to create a new SeqFeature database.

SYNOPSIS

        bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]]

       Try 'bp_seqfeature_load.pl --help' or '--man' for more information.

OPTIONS

       -d, --dsn
           DBI data source (default dbi:mysql:test)

       -n, --namespace
           The table prefix to use (default undef) Allows several independent sequence feature databases to be
           stored in a single database

       -s, --seqfeature
           The type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature)

       -a, --adaptor
           The storage adaptor (class) to use (default DBI::mysql)

       -v, --verbose
           Turn on verbose progress reporting (default true) Use --noverbose to switch this off.

       -f, --fast
           Activate fast loading. (default 0) Only available for some adaptors.

       -T, --temporary-directory
           Specify temporary directory for fast loading (default File::Spec->tmpdir())

       -i, --ignore-seqregion
           If true, then ignore ##sequence-region directives in the GFF3 file (default, create a feature for
           each region)

       -c, --create
           Create the database and reinitialize it (default false) Note, this will erase previous database
           contents, if any.

       -u, --user
           User to connect to database as

       -p, --password
           Password to use to connect to database

       -z, --zip
           Compress database tables to save space (default false)

       -S, --subfeatures
           Turn on indexing of subfeatures (default true) Use --nosubfeatures to switch this off.

       --fts
           Index the attribute table for full-text search (default false). Applicable only when --create is
           specified. Currently applicable to the DBI::SQLite storage adaptor only (using the most recent
           supported FTS indexing method, which may not be portable to older DBI::SQLite versions).

       --summary
           Generate summary statistics for coverage graphs (default false) This can be run on a previously
           loaded database or during the load. It will default to true if --create is used.

       -N, --nosummary
           Do not generate summary statistics to save some space and load time (default if --create is not
           specified, use this option to explicitly turn off summary statistics when --create is specified)

       --noalias-target
           Don't create an Alias attribute whose value is the target_id in a Target attribute (if the feature
           contains a Target attribute, the default is to create an Alias attribute whose value is the target_id
           in the Target attribute)

       Please see http://www.sequenceontology.org/gff3.shtml for information about the GFF3 format. BioPerl
       extends the format slightly by adding a ##index-subfeatures directive. Set this to a true value if you
       wish the database to be able to retrieve a feature's individual parts (such as the exons of a transcript)
       independently of the top level feature:

         ##index-subfeatures 1

       It is also possible to control the indexing of subfeatures on a case-by-case basis by adding "index=1" or
       "index=0" to the feature's attribute list. This should only be used for subfeatures.

       Subfeature indexing is true by default. Set to false (0) to save lots of database space and speed
       performance. You may use --nosubfeatures to force this.