bp_seqfeature_load.pl - 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.
- --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.