bio-img_metadata 0.0.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.8.0"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 1.8.4"
+  gem "bundler", ">= 1.0.21"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2013 Ben J. Woodcroft
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# bio-img_metadata
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-img_metadata.png)](http://travis-ci.org/wwood/bioruby-img_metadata)
+
+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
+
+```sh
+gem install bio-img_metadata
+```
+
+## Usage
+
+```ruby
+require 'bio-img_metadata'
+
+d = Bio::IMG::Metadata.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
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## 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.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-img_metadata"
+  gem.homepage = "http://github.com/wwood/bioruby-img_metadata"
+  gem.license = "MIT"
+  gem.summary = %Q{Reads metadata from Integrated Microbial Genomes (IMG) metadata files into a programmaticly useful state}
+  gem.description = %Q{Reads metadata from Integrated Microbial Genomes (IMG) metadata files into a programmaticly useful state.}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J. Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-img_metadata #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-img_metadata.rb

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+require 'csv'
+
+module Bio
+  class Lineage
+    attr_accessor :taxon_id, :domain, :kingdom, :phylum, :class_name, :order, :family, :genus, :species
+    
+    def genus_species
+      @genus+' '+@species
+    end
+  end
+end
+
+module Bio  
+  module IMG
+    class Lineage < Bio::Lineage
+      attr_accessor :definition_line
+      
+      # Hash of key => value for each column
+      attr_accessor :attributes
+    end
+    
+    # Acts like an array of Bio::IMG::Lineage objects
+    #
+    # Use TaxonomyDefinitionFile#read to read in a file downloaded through the IMG export system
+    class Metadata < Array
+      FIELD_NAMES_TO_CLASSIFICATIONS = {
+        'taxon_oid' => :taxon_id,
+        'Domain' => :domain,
+        'Phylum' => :phylum,
+        'Class' => :class_name,
+        'Order' => :order,
+        'Family' => :family,
+        'Genus' => :genus,
+        'Species' => :species,
+      }
+      
+      # Reads an img_taxonomy_file into a new TaxonomyDefinitionFile object. 
+      # This object is then an array of Bio::IMG::Lineage objects from that file
+      def self.read(img_taxonomy_filename_path)
+        all_lineages = TaxonomyDefinitionFile.new
+        
+        # taxon_oid       Domain  Status  Genome Name     Phylum  Class   Order   Family  Genus   Species Strain  Release Date    IMG Release
+        # 650716001       Archaea Finished        Acidianus hospitalis W1 Crenarchaeota   Thermoprotei    Sulfolobales    Sulfolobaceae   Acidianus       hospitalis      W1      2011-12-01      IMG/W 3.5
+        # 648028003       Archaea Finished        Acidilobus saccharovorans 345-15        Crenarchaeota   Thermoprotei    Acidilobales    Acidilobaceae   Acidilobus      saccharovorans  345-15  2011-01-01      IMG/W 3.3
+        # 646564501       Archaea Finished        Aciduliprofundum boonei T469    Euryarchaeota   Thermoplasmata  Thermoplasmatales       Aciduloprofundaceae     Aciduliprofundum        boonei  T469    2010-08-01      IMG/
+        #
+        # Have to use a simple line#split because regular CSV class is narky and IMG metadata files aren't perfectly respetable
+        headers = nil
+        header_indices = {}
+        File.open(img_taxonomy_filename_path).each_line do |line|
+          row = line.chomp.split("\t")
+          
+          # If this is the first header row
+          if headers==nil
+            headers = row
+            FIELD_NAMES_TO_CLASSIFICATIONS.each do |header, attribute|
+              header_indices[header] = headers.index(header)
+            end
+            
+          else
+            lineage = Bio::IMG::Lineage.new
+            lineage.definition_line = line.chomp
+            
+            # 0# 650716001
+            # 1# Archaea
+            # 2# Finished
+            # 3# Acidianus hospitalis W1
+            # 4# Crenarchaeota
+            # 5# Thermoprotei
+            # 6# Sulfolobales
+            # 7# Sulfolobaceae
+            # 8# Acidianus
+            # 9# hospitalis
+            # 10# W1
+            # 11# 2011-12-01
+            # 12# IMG/W 3.5
+            FIELD_NAMES_TO_CLASSIFICATIONS.each do |header, attribute|
+              value = row[header_indices[header]]
+              value = value.to_i if attribute == :taxon_id
+              lineage.send "#{attribute}=".to_sym, value
+            end
+            
+            lineage.attributes = {}
+            row.each_with_index do |col, i|
+              lineage.attributes[headers[i]] = col
+            end
+            
+            all_lineages.push lineage
+          end
+        end
+        
+        return all_lineages
+      end
+      
+      # Return a hash, indexed by taxon_oid
+      def to_hash
+        hash = {}
+        each do |taxon|
+          hash[taxon.taxon_id] = taxon
+        end
+        return hash
+      end
+    end
+    
+    TaxonomyDefinitionFile = Metadata #Some backwards compatibility
+  end
+end

data/spec/bio-img_metadata_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioImgMetadata" do
+  DATA_DIR = File.join File.dirname(__FILE__), 'data'
+  
+  it "simple" do
+    d = Bio::IMG::TaxonomyDefinitionFile.read(File.join DATA_DIR, 'head.metadata.csv')
+    d.kind_of?(Array).should == true
+    d.length.should == 9
+    d[0].kind_of?(Bio::Lineage).should == true
+    
+    d[0].domain.should == 'Archaea'
+    d[0].attributes['Status'].should == 'Finished'
+    d[1].taxon_id.should == 2515075008
+  end
+  
+  it 'should have class equivalency TaxonomyDefinitionFile, MetadataFile' do
+    Bio::IMG::TaxonomyDefinitionFile.should == Bio::IMG::Metadata
+  end
+end

data/spec/data/head.metadata.csv

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+taxon_oid	Domain	Status	Proposal Name	Genome Name / Sample Name	Sequencing Center	Phylum	Class	Order	Family	Genus	Species	Genome ID	NCBI Taxon ID	RefSeq Project ID	GenBank Project ID	Strain	Funding Agency	Add Date	Is Public	Release Date	IMG Release	IMG Product Assignment	IMG Submission ID	Proposal GOLD ID	Altitude	Biotic Relationships	Body Site	Body Subsite	Cell Arrangement	Cell Shape	Contact Email	Contact Name	Diseases	Ecosystem	Ecosystem Category	Ecosystem Subtype	Ecosystem Type	Energy Source	Funding Program	Geographic Location	Gram Staining	Host Gender	Host Name	IMG Project ID	Isolation	Isolation Country	Latitude	Longitude	Metabolism	Motility	Oxygen Requirement	Phenotype	Relevance	Salinity	Specific Ecosystem	Sporulation	Temperature Range	Uncultured Type	Genome Size (Number of total bases)	Gene Count (Number of total Genes)	Scaffold Count (Number of scaffolds)	CRISPR Count (Number of CRISPRs)	GC Count (Number of GC)	GC % (Percentage of GC)	Coding Base Count (Total number of coding bases)	CDS Count (Number of CDS genes)	CDS % (Percentage of CDS genes)	RNA Count (Number of RNA genes)	RNA %	rRNA Count (Number of rRNA genes)	5S rRNA Count (Number of 5S rRNAs)	16S rRNA Count (Number of 16S rRNAs)	18S rRNA Count (Number of 18S rRNAs)	23S rRNA Count (Number of 23S rRNAs)	28S rRNA Count (Number of 28S rRNAs)	tRNA Count (Number of tRNA genes)	Other RNA Count (Number of other unclassified RNA genes)	Pseudo Genes Count (Number of pseudo genes)	Pseudo Genes % (Percentage of pseudo genes)	Unchar Count (Number of uncharacerized genes)	Unchar % (Percentage of uncharacterized genes)	Dubious Count	Dubious %	w/ Func Pred Count (Number of genes with predicted protein product)	w/ Func Pred % (Percentage of genes with predicted protein product)	w/o Func Pred Sim Count (Number of genes without function prediction with similarity)	w/o Func Pred Sim % (Percentage of genes without predicted protein product with similarity)	w/o Func Pred No Sim Count (Number of genes without function prediction without similarity)	w/o Func Pred No Sim % (Percentage of genes without function prediction without similarity)	Orthologs Count	Orthologs %`	Paralogs Count	Paralogs %	Obsolete Count (Number of obsolete genes)	Obsolete % (Percentage of obsolete genes)	Revised Count (Number of revised genes)	Revised % (Percentage of revised genes)	Fused Count (Number of fused genes)	Fused % (Percentage of fused genes)	Fusion Component Count (Number of genes involved as fusion components)	Fusion component % (Genes involved as fusion components percentage)	SwissProt Count (Number of genes in SwissProt protein product)	SwissProt % (Percentage of genes in SwissProt protein product)	Not SwissProt Count (Number of genes not in SwissProt protein product)	Not SwissProt % (Percentage of genes not in SwissProt protein product)	SEED Count (Number of genes in SEED)	SEED % (Percentage of genes in SEED)	Not SEED Count (Number of genes not in SEED)	Not SEED % (Percentage of genes not in SEED)	COG Count (Number of genes in COG)	COG % (Percentage of genes in COG)	KOG Count (Number of genes in KOG)	KOG % (Percentage of genes in KOG)	Pfam Count (Number of genes in Pfam)	Pfam % (Percentage of genes in Pfam)	TIGRfam Count (Number of genes in TIGRfam)	TIGRfam % (Percentage of genes in TIGRfam)	InterPro Count (Number of genes in InterPro)	InterPro % (Percentage of genes in InterPro)	Enzyme Count (Number of genes assigned to enzymes)	Enzyme % (Percentage of genes assigned to enzymes)	TC Count (Number of genes assigned to Transporter Classification)	TC % (Percentage of genes assigned to Transporter Classification)	KEGG Count (Number of genes in KEGG)	KEGG % (Percentage of genes in KEGG)	Not KEGG Count (Number of genes not in KEGG)	Not KEGG % (Percentage of genes not in KEGG)	KO Count (Number of genes in KEGG Orthology (KO))	KO % (Percentage of genes in KEGG Orthology (KO))	Not KO Count (Number of genes not in KEGG Orthology (KO))	Not KO % (Percentage of genes not in KEGG Orthology (KO))	MetaCyc Count (Number of genes in MetaCyc)	MetaCyc % (Percentage of genes in MetaCyc)	Not MetaCyc Count (Number of genes not in MetaCyc)	Not MetaCyc % (Percentage of genes not in MetaCyc	IMG Term Count (Number of genes with IMG terms)	IMG Term % (Percentage of genes with IMG terms)	IMG Pathwawy Count (Number of genes in IMG pathwawys)	IMG Pathway % (Percentage of genes in IMG pathways)	IMG Parts List Count (Number of genes in IMG parts list)	IMG Parts List % (Percentage of genes in IMG parts list)	MyIMG Annotation Count	MyIMG Annotation %	Signal Peptide Count (Number of genes coding signal peptides)	Signal Peptide % (Percentage of genes coding signal peptides)	Transmembrane Count (Number of genes coding transmembrane proteins)	Transmembrane % (Percentage of genes coding transmembrane proteins)	Horizontally Transferred Count	Horizontally Transferred %	Genome Property Count (Number of genes in Genome Properties)	Genome Property % (Percentage of genes in Genome Properties)	Ortholog Group Count	Paralog Group Count	COG Cluster Count (Number of COG clusters)	KOG Cluster Count (Number of KOG clusters)	Pfam Cluster Count (Number of Pfam clusters)	TIGRfam Cluster Count (Number of TIGRfam clusters)	IMG Cluster Count	IMG Cluster %	Chromosomal Cassette Gene Count	Chromosomal Cassette Gene %	Chromosomal Cassette Count
+644736411	Archaea	Finished	Thermococcus gammatolerans EJ3	Thermococcus gammatolerans EJ3	DOE Joint Genome Institute	Euryarchaeota	Thermococci	Thermococcales	Thermococcaceae	Thermococcus	gammatolerans	644736411	593117	59389	33671	EJ3		2009-10-13	Yes	2009-12-01	IMG/W 3.0			Gc01034		Free living				Coccus-shaped	NCKyrpides@lbl.gov	NIKOS	None					Organotroph		oil wells of the Samotlor oil reservoir	Gram-			14544	hydrothermal vent chimneys located in the mid-Atlantic Ridge and Guyamas basin.					Motile	Anaerobe	Radiation resistant	Biotechnological			Nonsporulating	Hyperthermophile		2045438	2206	1		1095567	0.54	1910049	2156	97.73	50	2.27	4	2	1	0	1	0	46	0	0	0	0	0	0	0	1427	64.69							1030	46.69	0	0	0	0	99	4.49	708	32.09	178	8.07	1978	89.66	2	0.09	2154	97.64	1524	69.08	757	34.32	1655	75.02	554	25.11	1681	76.2	472	21.4	199	9.02	529	23.98	1627	73.75	1047	47.46	1109	50.27	450	20.4	1706	77.33	554	25.11	161	7.3	193	8.75	0	0	285	12.92	561	25.43	70	3.17	0	0			1071	525	1156	505			2206	100	66
+2515075008	Archaea	Permanent Draft	Continuation of the Genomic Encyclopedia of Bacteria and Archaea pilot project	Methanolobus tindarius DSM 2278	DOE Joint Genome Institute	Euryarchaeota	Methanomicrobia	Methanosarcinales	Methanosarcinaceae	Methanolobus		2515075008	1090322				DOE; DSMZ	2012-06-29	Yes	2012-06-29		Yes	9393	Gi02920		Free living				Coccus-shaped	NCKyrpides@lbl.gov	NIKOS	None						DOE-CSP 2011	Sediment from Lakes of Marinello, Italy	Gram-			13501	Sediment from Lakes of Marinello, Italy	Italy	38.132591	15.05422	Methanogen		Anaerobe		Tree of Life, GEBA				Mesophile		3151883	3022	1		1254128	0.4	2767116	2957	97.85	65	2.15	9	3	3	0	3	0	50	6	34	1.13	0	0	0	0	2184	72.27							1124	37.19	0	0	0	0	5	0.17	0	0	0	0	2957	97.85	0	0	2957	97.85	2204	72.93	974	32.23	2219	73.43	889	29.42	2282	75.51	643	21.28	303	10.03	776	25.68	2181	72.17	1354	44.8	1603	53.04	624	20.65	2333	77.2	641	21.21	226	7.48	202	6.68	0	0	441	14.59	782	25.88	0	0	0	0			1352	589	1459	711			3022	100	256
+2512047039	Archaea	Finished	Pyrobaculum oguniense TE7	Pyrobaculum oguniense TE7, DSM 13380	UCSC	Crenarchaeota	Thermoprotei	Thermoproteales	Thermoproteaceae	Pyrobaculum		2512047039	698757	84411	42375			2012-03-23	Yes	2012-03-23		No	7574	Gc02118						Rod-shaped	NCKyrpides@lbl.gov	NIKOS						Heterotroph		Oguni-cho, Kumamoto, Japan 				559	Terrestrial hot spring at Oguni-cho, Kumamoto, Japan 	Japan	32.806322	130.718651			Facultative						Hyperthermophile		2452920	3014	2		1350357	0.55	2154879	2869	95.19	145	4.81	3	1	1	0	1	0	48	94	34	1.13	0	0	0	0	1709	56.7							931	30.89	0	0	0	0	3	0.1	0	0	0	0	2869	95.19	0	0	2869	95.19	1757	58.29	790	26.21	1743	57.83	494	16.39	1804	59.85	559	18.55	210	6.97	670	22.23	2199	72.96	1107	36.73	1762	58.46	539	17.88	2330	77.31	485	16.09	168	5.57	168	5.57	0	0	775	25.71	630	20.9	0	0	0	0			1105	549	1100	460			3014	100	206
+650716053	Archaea	Finished	Genome sequencing and comparison of novel methanogens from peatlands and bioreactors	Methanobacterium sp. SWAN-1	DOE Joint Genome Institute	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobacterium	sp.	650716053	868131	67359	53561	SWAN-1		2011-08-22	Yes	2011-12-01	IMG/W 3.5			Gc01780		Free living					ipagani@lbl.gov	Ioanna Pagani	None					Lithotroph	DOE-CSP 2010		Gram-			17802					Methanogen				Bioenergy, Biotechnological, Comparative analysis				Mesophile		2546541	2500	1		909924	0.36	2010186	2442	97.68	58	2.32	9	3	3	0	3	0	47	2	45	1.8	0	0	0	0	1536	61.44							1151	46.04	0	0	0	0	43	1.72	0	0	0	0	2442	97.68	0	0	2442	97.68	1838	73.52	787	31.48	1879	75.16	704	28.16	1869	74.76	576	23.04	205	8.2	707	28.28	1735	69.4	1149	45.96	1293	51.72	553	22.12	1889	75.56	490	19.6	176	7.04	162	6.48	0	0	490	19.6	589	23.56	240	9.6	0	0			1218	509	1288	625			2500	100	456
+650377982	Archaea	Finished	Sulfolobus islandicus REY15A	Sulfolobus islandicus REY15A	Los Alamos National Lab	Crenarchaeota	Thermoprotei	Sulfolobales	Sulfolobaceae	Sulfolobus	islandicus	650377982	930945	162071	60485	REY15A		2011-03-26	Yes	2011-07-01	IMG/W 3.4			Gc01624		Free living			Singles	Coccus-shaped	ipagani@lbl.gov	Ioanna Pagani	None					Lithotroph			Gram-			18556						Nonmotile	Facultative	Acidophile	Biotechnological			Nonsporulating	Hyperthermophile		2522992	2753	1		890812	0.35	2177858	2644	96.04	109	3.96	4	1	1	0	1	0	45	60	0	0	0	0	0	0	1812	65.82							1184	43.01	0	0	0	0	97	3.52	0	0	0	0	2644	96.04	55	2	2589	94.04	1914	69.52	935	33.96	1922	69.81	588	21.36	1983	72.03	577	20.96	216	7.85	643	23.36	2001	72.68	1056	38.36	1588	57.68	558	20.27	2086	75.77	191	6.94	104	3.78	57	2.07	0	0	474	17.22	577	20.96	5	0.18	0	0			1122	579	1165	496			2753	100	252
+649633040	Archaea	Finished	A Genomic Encyclopedia of Bacteria and Archaea (GEBA)	Desulfurococcus mucosus 07/1, DSM 2162	DOE Joint Genome Institute	Crenarchaeota	Thermoprotei	Desulfurococcales	Desulfurococcaceae	Desulfurococcus	mucosus	649633040	765177	62227	48641	DSM 2162		2011-03-26	Yes	2011-07-01	IMG/W 3.4			Gc01595	1,053 m	Free living				Sphere-shaped	NCKyrpides@lbl.gov	NIKOS	None					Organotroph	DOE-GEBA 2007	Askja, Iceland	Gram-			13494	Hot solfataric spring; Iceland	Iceland	65.05	-16.8	Sulfur respiration	Nonmotile	Anaerobe		Tree of Life, Biotechnological, GEBA			Nonsporulating	Hyperthermophile		1314639	1421	1		698621	0.53	1186786	1371	96.48	50	3.52	3	1	1	0	1	0	46	1	26	1.83	0	0	0	0	934	65.73							438	30.82	0	0	0	0	48	3.38	0	0	0	0	1371	96.48	0	0	1371	96.48	1075	75.65	541	38.07	1042	73.33	346	24.35	1057	74.38	329	23.15	138	9.71	406	28.57	965	67.91	754	53.06	617	43.42	320	22.52	1051	73.96	234	16.47	69	4.86	90	6.33	0	0	323	22.73	294	20.69	63	4.43	0	0			799	418	838	329			1421	100	61
+649989953	Archaea	Draft	Haladaptatus paucihalophilus DX253	Haladaptatus paucihalophilus DX253	Oklahoma State University	Euryarchaeota	Halobacteria	Halobacteriales	Halobacteriaceae	Haladaptatus	paucihalophilus	649989953	797209	62523	50445	DX253		2011-03-26	Yes	2011-07-01	IMG/W 3.4			Gi07306					Clusters	Coccus-shaped	ipagani@lbl.gov	Ioanna Pagani	None					Chemoorganotroph		Zodletone Spring, Oklahoma	Gram-			17533	Low-salt, sulfide- and sulfur-rich spring (Zodletone Spring) in south-western Oklahoma, USA	USA	34.996	-98.688			Aerobe		Biotechnological	Halophile			Mesophile		4284805	4496	32		2648659	0.62	3649979	4443	98.82	53	1.18	6	2	3	0	1	0	47	0	0	0	0	0	1	0.02	2528	56.23							2436	54.18	0	0	1	0	246	5.47	0	0	0	0	4443	98.82	0	0	4443	98.82	2986	66.41	1391	30.94	3008	66.9	836	18.59	3097	68.88	831	18.48	493	10.97	950	21.13	3493	77.69	1690	37.59	2753	61.23	809	17.99	3634	80.83	780	17.35	276	6.14	260	5.78	0	0	1106	24.6	1111	24.71	152	3.38	0	0			1401	708	1521	634			4496	100	445
+638154510	Archaea	Finished	Methanothermobacter thermoautotrophicus Delta H	Methanothermobacter thermoautotrophicus Delta H	J. Craig Venter Institute	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanothermobacter	thermautotrophicus	638154510	187420	57877	289	str. Delta H	DOE	2006-10-02	Yes	2006-12-01	IMG/W 2.0			Gc00009		Free living					NCKyrpides@lbl.gov	NIKOS	None					Lithoautotroph, Autotroph, Lithotroph		Sewage sludge in 1971 in Urbana Illinois	Gram-			10677	Sewage sludge in 1971 in Urbana Illinois	USA	40.106649	-88.195627	Methanogen	Nonmotile	Obligate anaerobe		Biotechnological, Energy production			Nonsporulating	Thermophile		1751377	1893	1		867701	0.5	1570117	1845	97.46	48	2.54	7	3	2	0	2	0	39	2	23	1.22	0	0	35	1.85	1362	71.95							929	49.08	87	5	155	8	108	5.71	726	38.35	191	10.09	1654	87.37	1106	58.43	739	39.04	1458	77.02	637	33.65	1529	80.77	631	33.33	1544	81.56	533	28.16	147	7.77	637	33.65	1208	63.81	1047	55.31	798	42.16	514	27.15	1331	70.31	630	33.28	224	11.83	192	10.14	2	0.11	157	8.29	188	9.93	90	4.75	0	0			1125	477	1193	608			1980	104.6	63
+637000162	Archaea	Finished	Methanosarcina barkeri fusaro	Methanosarcina barkeri Fusaro, DSM 804	DOE Joint Genome Institute	Euryarchaeota	Methanomicrobia	Methanosarcinales	Methanosarcinaceae	Methanosarcina	barkeri	637000162	269797	57715	103	str. fusaro	DOE	2006-10-02	Yes	2006-12-01	IMG/W 2.0			Gc00295		Free living			Singles	Coccus-shaped	NCKyrpides@lbl.gov	NIKOS	None					Lithotroph	DOEM 2001	Naples Italy	Gram-			10390	Mud samples from Lago del Fusaro Lake in Naples Italy	Italy	40.844	14.251	Methanogen	Nonmotile	Anaerobe		Energy production, Environmental, Biotechnological, Carbon cycle			Nonsporulating	Mesophile		4873766	3834	2		1912156	0.39	3406841	3758	98.02	76	1.98	9	3	3	0	3	0	62	5	134	3.5	0	0	3	0.08	1820	47.47							2631	68.62	0	0	3	0	256	6.68	1567	40.87	329	8.58	3429	89.44	3631	94.71	127	3.31	2703	70.5	1153	30.07	2927	76.34	1026	26.76	2843	74.15	756	19.72	436	11.37	900	23.47	2858	74.54	1619	42.23	2139	55.79	733	19.12	3025	78.9	811	21.15	271	7.07	255	6.65	1	0.03	543	14.16	957	24.96	305	7.96	0	0			1409	629	1524	749			3834	100	887

data/spec/spec_helper.rb

@@ -0,0 +1,12 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-img_metadata'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

@@ -0,0 +1,130 @@
+--- !ruby/object:Gem::Specification
+name: bio-img_metadata
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-01-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &80862770 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: *80862770
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &80862450 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *80862450
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &80861630 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: *80861630
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &80861100 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: *80861100
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &80860260 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *80860260
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &80859920 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *80859920
+description: Reads metadata from Integrated Microbial Genomes (IMG) metadata files
+  into a programmaticly useful state.
+email: donttrustben near gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .rspec
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/bio-img_metadata.rb
+- spec/bio-img_metadata_spec.rb
+- spec/data/head.metadata.csv
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/bioruby-img_metadata
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 591437005
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.17
+signing_key: 
+specification_version: 3
+summary: Reads metadata from Integrated Microbial Genomes (IMG) metadata files into
+  a programmaticly useful state
+test_files: []