A gem to use the Distributed Annotation System with Ruby.
The Distributed Annotation System is a protocol developed to allow the distributed annotation of nucleotide and protein sequences. DAS servers are used to deliver reference sequences and/or annotations for those sequences. DAS clients can be used to remix the information from different sources and deliver a single representation of the information. Examples for DAS-clients are ENSEMBL Genome Browser, Spice and Dalliance.
RubyDAS tries to provide a reference- and annotation-server with the DAS 1.6 standard based on Ruby. Reference-sequences and the annotations are stored in a database of choice using Datamapper. The dependencies of RubyDAS as of now are:
- Read GFF3
- Read FASTA
- DAS sequences-command
- DAS sources-command
- DAS features-commands
To test the current implementation just run server.rb and point your browser to localhost:4567/das/rubydas/sequence?segment=MAL5:1000,2000 localhost:4567/das/rubydas/types?segment=MAL5:1000,2000 or localhost:4567/das/rubydas/features?segment=MAL5:1000,2000
- Implement entry_points
- Implement sources
- Add further input-file-formats
- Test compatibility with DAS-clients
If you are interested in joining the development of RubyDAS you can join the Google Group/mailinglist at https://groups.google.com/group/rubydas