bp_seqfeature_load.pl(1) Load GFF into a SeqFeature database


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.


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

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


-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.
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)
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.