simple sql dump is fast, and reliable in getting all mapped features by keeping logic simple.

using simple sql to dump all db features to intermediate table allows easy checks that all features get to bulk files.

Here are some reasons we take this approach:

postprocess these table files to create the various public use formats (the time-consuming and configurable part), organized into per-chromosome files.

The feature info is simple: type, location, name/id, and a few attributes (db_xrefs.)

dump all Chado db features using simple (and quick) sql, to common intermediate table files, and chromosome dna to raw files.

Why use this package rather than using other middleware layers to Chado db - Chado XML, Chado::AutoDBI, BioPerl, ? The general logic is Fasta sequence for each selected feature set, with headers from feature filesĪdditional genome outputs can be added with Perl adaptor packages from a Bulkfiles base adaptor object.DNA files (full chromosomes) in raw and fasta formats.These are current primary outputs, which are configurable to suit project needs. It produces all the contents needed for a GMOD Standard URL genome data download folder. Once tuned to your project's needs with its organism and site configurations, it can generate public data releases on a regular basis. It works with several FlyBase Chado releases, with SGDLite, and has been tested with other Chado databases. Bulkfiles is a GMOD Perl package that generates Fasta, GFF3, DNA and other bulk genome annotation files from Chado databases.

Gmod file converter