bio-express_beta_diversity

Ruby interface to express beta diversity things. Currently, functionality is limited to parsing the output distance matrices, and input "OTU table" format.

Note: this software is under active development!

gem install bio-express_beta_diversity

Parsing the distance matrix:

require 'bio-express_beta_diversity'

dists = Bio::EBD::DistanceMatrix.parse_from_file 'Bray-Curtis.cluster.diss'
dists.sample_names #=> ["sample1", "sample2", ... ]
dists.distance('sample1','sample2') #=> 0.251761
dists.distance('sample2','sample1') #=> 0.251761

Parsing the input OTU table:

otus = Bio::EBD::Format.parse_from_file 'my.ebd'
otus.sample_counts.keys #=> ['sample1','sample2', ..]
otus.sample_counts['sample1'] #=> [1.0,4.0,0.0,..]
otus.otu_names #=> ['otu1','otu2','otu3',..]

The otu_names correspond with the order of the sample_counts.values.

The API doc is online. For more code examples see the test files in the source tree.

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/wwood/bioruby-express_beta_diversity

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 (http://biogems.info/index.html#bio-express_beta_diversity)

Copyright (c) 2013 Ben J. Woodcroft. See LICENSE.txt for further details.