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BP_SEQFEATURE_LOAD(1)                      User Contributed Perl Documentation


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.

       --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.

perl v5.20.2                      2015-09-15             BP_SEQFEATURE_LOAD(1)

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