bio-img_metadata

Build Status

Reads metadata from Integrated Microbial Genomes (IMG) metadata files. Metadata files are generated by searching for one or more taxons, and then exporting various/all genome-specific characters e.g. kingdom, genus, temperature range, taxon identifier, etc.

Installation

gem install bio-img_metadata

Usage

require 'bio-img_metadata'

d = Bio::IMG::.read(File.join DATA_DIR, 'head.metadata.csv') #=> an Array of Bio::IMG::Metadata objects

d.length.should == 9 #=> The array has 9 members, one for each line in the metadata file
d[0].kind_of?(Bio::IMG::Lineage).should == true #=> Each lineage's object

d[0].domain.should == 'Archaea' #=> some attributes are now methods (mostly the taxonomy-related ones)
d[1].taxon_id.should == 2515075008

d[0].attributes['Status'].should == 'Finished' #=> the rest are in the attributes array

Project home page

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

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

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

Copyright

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