Note: this software is under active development!
This is currently an early work in progress to create a parallel GFF3 and GTF parser library for D and a Ruby gem which would take advantage of that library.
TODO: Write scripts for installation.
A D compliler is required to run the tests.
If you are using homebrew on OsX you can install dmd like so:
$ brew install dmd
Currently only D unit tests are working. You can run them using the "unittests" rake task, like this:
rake unittests require 'bio-hpc-gff3'TODO: Generate API docs and find a nice place for them somewhere on the net.
The API doc is online. For more code examples see the test files in the source tree.
The validation utility can be built using the "validator" rake task, like this:
rake validatorThe result will be in the root directory, and can be used like this:
./validate-gff3 path/to/file.gff3There is a small D application for performance benchmarking, you can build it using:
rake benchmarkAnd then run it like this:
./benchmark-gff3 path/to/file.gff3The most basic case for the banchmarking utility is to parse the file into records. More functionality is available using command line options:
-v turn on validation
-r turn on replacement of escaped characters
-f merge records into features
-c N feature cache size (how many features to keep in memory), default=1000
-l link feature into parent-child relationships
Information on the source tree, documentation, examples, issues and how to contribute, see
http://github.com/mamarjan/bioruby-hpc-gff3
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
If you use this software, please cite one of
- BioRuby: bioinformatics software for the Ruby programming language
- Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
This Biogem is published at #bio-hpc-gff3
Copyright (c) 2012 Marjan Povolni. See LICENSE.txt for further details.