A PERL script collection to convert and export FPD database information to GFF3 format for use in GBrowse 2.
- Modular
- Multi-process, scalable across many CPUs
- PERL 5.8+
- Perl modules:
- FPD
- Thread::Queue
- forks
run.pl [options] (instance)
(instance) is the FPD/GBrowse instance to use. The name corresponds to the directory in /home/fpd/deployed
options:
-t,--threads number of worker "threads" to use
-h,--help show help message
-v,--verbose show verbose output
For each instance, the script dumps the list of features from the gbrowse/fgroup database table and populates a work queue. The specified number of workers (default 4) are then spawned to eat through the work queue, taking each feature and placing it in a GFF3 format file corresponding to the feature type and dataset number.