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.