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GFF3 plugin for BioRuby - allows parsing big data GFF3
Ruby Perl
tag: v0.8.2

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README.rdoc

bio-gff3

GFF3 parser, aimed at parsing big data GFF3 to return sequences of any type, including assembled mRNA, protein and CDS sequences.

Features:

# Take GFF3 (genome browser) information of any type, and assemble sequences, e.g. mRNA and CDS # Options for low memory use and caching of records # Support for external FASTA input files # Use of multi-cores (NYI)

Currently the output is a FASTA file.

You can use this plugin in two ways. First as a standalone program, next as a plugin library to BioRuby.

Install and run gff3-fetch

After installing ruby 1.9, or later, you can use rubygems

gem install bio-gff3

Then, fetch mRNA and CDS information from GFF3 files and output to FASTA:

gff3-fetch mrna test/data/gff/test.gff3
gff3-fetch cds test/data/gff/test.gff3

Development

To use the library

require 'bio-gff3'

For coding examples see ./bin/gff3-fetch and the ./spec/*rb

You can run RSpecs with something like

rspec -I ../bioruby/lib/ spec/*.rb

(supposing you are referring a bioruby source repository)

This implementation depends on BioRuby's basic GFF3 parser, with the possible advantage that the plugin can assemble sequences, is faster and does not consume all memory. The Gff3 specs are based on the output of the Wormbase genome browser.

See also

gff3-fetch --help

For a write-up see thebird.nl/bioruby/BioRuby_GFF3.html


Copyright

Copyright (C) 2010,2011 Pjotr Prins <pjotr.prins@thebird.nl>

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