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A fast parallel GFF3 parser

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README.md

bio-hpc-gff3

Build Status

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.

Installation

TODO: Write scripts for installation.

Run tests

Currently only D unit tests are working. You can run them using the "unittests" rake task, like this:

    rake unittests

Usage

    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.

GFF3 File validation

The validation utility can be built using the "validator" rake task, like this:

    rake validator

The result will be in the root directory, and can be used like this:

    ./validate-gff3 path/to/file.gff3

Benchmarking utility

There is a small D application for performance benchmarking, you can build it using:

    rake benchmark

And then run it like this:

    ./benchmark-gff3 path/to/file.gff3

The 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

Project home page

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.

Cite

If you use this software, please cite one of

Biogems.info

This Biogem is published at #bio-hpc-gff3

Copyright

Copyright (c) 2012 Marjan Povolni. See LICENSE.txt for further details.

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