reubypathdb 0.1.0

data/.document

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+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC

data/LICENSE

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+Copyright (c) 2009 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.rdoc

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+= eupathdb
+
+Description goes here.
+
+== Note on Patches/Pull Requests
+ 
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Commit, do not mess with rakefile, version, or history.
+  (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
+
+== Copyright
+
+Copyright (c) 2010 Ben J Woodcroft. See LICENSE for details.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "reubypathdb"
+    gem.summary = %Q{Classes to help parsing EuPathDB data files}
+    gem.description = %Q{Classes to help parsing EuPathDB data files}
+    gem.email = "donttrustben near gmail.com"
+    gem.homepage = "http://github.com/wwood/reubypathdb"
+    gem.authors = ["Ben J Woodcroft"]
+    gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
+end
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/test_*.rb'
+    test.verbose = true
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+task :test => :check_dependencies
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "reubypathdb #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/eupathdb_gene_information_table.rb

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+
+class EuPathDBGeneInformationTable
+  include Enumerable
+
+  def initialize(io)
+    @io = io
+  end
+
+  def each
+    while g = next_gene
+      yield g
+    end
+  end
+
+  # Returns a EuPathDBGeneInformation object with all the data you could
+  # possibly want.
+  def next_gene
+    info = EuPathDBGeneInformation.new
+
+    # first, read the table, which should start with the ID column
+    line = @io.readline.strip
+    while line == ''
+      return nil if @io.eof?
+      line = @io.readline.strip
+    end
+
+    while line != ''
+      if matches = line.match(/^(.*?)\: (.*)$/)
+        info.add_information(matches[1], matches[2])
+      else
+        raise Exception, "EuPathDBGeneInformationTable Couldn't parse this line: #{line}"
+      end
+      
+      line = @io.readline.strip
+    end
+
+    # now read each of the tables, which should start with the
+    # 'TABLE: <name>' entry
+    line = @io.readline.strip
+    table_name = nil
+    headers = nil
+    data = []
+    while line != '------------------------------------------------------------'
+      if line == ''
+        # add it to the stack unless we are just starting out
+        info.add_table(table_name, headers, data) unless table_name.nil?
+
+        # reset things
+        table_name = nil
+        headers = nil
+        data = []
+      elsif matches = line.match(/^TABLE\: (.*)$/)
+        # name of a table
+        table_name = matches[1]
+      elsif line.match(/^\[.*\]/)
+        # headings of the table
+        headers = line.split("\t").collect do |header|
+          header.gsub(/^\[/,'').gsub(/\]$/,'')
+        end
+      else
+        # a proper data row
+        data.push line.split("\t")
+      end
+      line = @io.readline.strip
+    end
+
+    # return the object that has been created
+    return info
+  end
+end
+
+class EuPathDBGeneInformation
+  def info
+    @info
+  end
+
+  def get_info(key)
+    @info[key]
+  end
+  alias_method :[], :get_info
+
+  def get_table(table_name)
+    @tables[table_name]
+  end
+
+  def add_information(key, value)
+    @info ||= {}
+    @info[key] = value
+    "Added info #{key}, now is #{@info[key]}"
+  end
+
+  def add_table(name, headers, data)
+    @tables ||= {}
+    @tables[name] = []
+    data.each do |row|
+      final = {}
+      row.each_with_index do |cell, i|
+        final[headers[i]] = cell
+      end
+      @tables[name].push final
+    end
+  end
+end

data/test/data/eupathGeneInformation.txt

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+ID: TGME49_000010
+Gene Group: TG_9133
+Data Source: T.gondii ME49 contigs from Genbank
+Genomic Sequence ID: TGME49_chrXII
+Chromosome: XII
+Genomic Location: TGME49_chrXII: 2,230,843 - 2,234,577 (-)
+Gene Strand: reverse
+Gene Type: protein coding
+# Exons: 2
+Transcript Length: 3391
+CDS Length: 1242
+Product Description: hypothetical protein
+Protein Length: 413
+# TM Domains: 0
+Molecular Weight: 45197
+Isoelectric Point: 7.92
+EC Numbers: null
+Ortholog count: 3
+Paralog count: 2
+Temporary Ortholog Group: OG3_85809
+Total SNPs All Strains: 5
+Nonsynonymous SNPs All Strains: 1
+Synonymous SNPs All Strains: 0
+Nonsyn/Syn SNP Ratio All Strains: 0
+SignalP Scores: null
+SignalP Peptide: null
+Annotated GO Function: null
+Annotated GO Process: null
+Annotated GO Component: null
+Predicted GO Function: null
+Predicted GO Process: null
+Predicted GO Component: null
+TypeIII / TypeI fold-change: -11.6288769802844
+TypeIII / TypeII fold-change: -7.03490049704923
+TypeII / TypeI fold-change: -1.65302650480445
+Organism: Toxoplasma gondii ME49
+Release4 IDs: 1.m00014
+= Release4 Protein?: Yes
+Predicted Protein Sequence: MHSRNCVGGSFYDGAVCCSPPSRAFGNMHNLVLVLLAFLSSWEDNETRRGDVVEQQNPFRLAIHGKTERDRDGNCTQHGVRSNDFRFVDEGDMSAEVGRGLALQKHVRVPLQASIARRLSDRESEKRSQGSDNGNGTTPPLPPRRTPSPRPSGASGVVQQGAAGVGTPTMLGTGGQHLSDQGATGSVAPSVQSSSSSAVSVEGALPLIQFFGSRSSSPEVPLCHACHTVEAAVGVLQSIRHRRRAGAREAAERIAALESQHALLVSSSTQGEHSQGARPSDILVSHRALQRARREATRQEETLRGEEASLEAFIRVASEKREREGQRSLEVLRQRVENQTAELAVLRVEAALERQREMVELERRRGDLLALALVAEDDEEYLRLSAEEEAVQRQIEQLAEETRRPRRGRRKPA
+Predicted RNA/mRNA Sequence (introns spliced out): TCTCACGTGAACCGGCCCCAACTGAGGAACACATACGACGGTGGAACCAGGGTGCAGTCGGCACGTCGCTAGGGTTCGTTATTCTGCACCACTGTCTGATTTGGCTGTGCGCCCGAATCTGTGGAACACGTGCACTCGCGAATATTCATGAGAACACATTGTTTTGGAATCAACTAGCCAAATCCTTCCCTCTGCCACACATGCTGAAAGACGAGCTTGGGGGTGAAAGCTCTACTTCAACAAACGCACGGGCAGACGGTTCTCACATGTGCGACGTCGCTAGACGAGTTCGAAGTCGTAGACATCATACTTTTGGGTTGTGTGTGAAGTTAACAACTAACCACTAGATACGTGTTCTGAACAACCGGGAACACCGGACAGGCGCCCACTGCTTTCTGGATAACAAACGAATGGAGGAAGCTCAGCCGCACAGCTTCTTCTGGAGGACTGGGAGAGAAGTGGTCCGACAGAGGCTCAGCTTCGAAACGGTTTTGTGGGCTTTAGTTCTGAACTGAGCTTTTTTTGTTCGACTCATCACCCCAAAATCAAGACTCGGTTGATACATCAGCCGAAGTTGGGGCGGGCTGACGACACCTTAAACGTTCACAGAGACGAGAGAACCCGTTCTCCCGGTGTTGCAATTCATGCTGGGAATCCCCGATGTATGGGGATACAGCTTCAGAGCGAGCCACCACCACCAAGGTTGCCGTTGATGCGGCAGTGACGCGAAGTAGAAGAGCGAAAGAGTGTGCCAATACTTTTGTCTGTTTCACGTGTTTTAAATTGAAGCAACACCGTTCACTCATGCATTTCGCGCCACAGAAGCAGGTAGCAGAGAACCAAAGTTTATTCGCTAACAATTGAACAACACAAGGATACAATCGAGGATCATCGCCACGCAAGTTGGGATCACGGGCCGACTTCAAACAAACGAGGGGTGTACGTGCGAGGGCCCCTGTTCAGCGACGCGTAGTTCCTGCCATGTACACACTTCAGTACTCGTATGAATCCGTTCACGTTGCCGCTGTTTTGTGATTTAGCGTACAATTTTCAAACAGACGAAAGCTACAAATGCTGTACAGGGATAGACATGATGCGGTGTCTTTCCTATCTCTGTCTTGGGTCGGACCTATCCTTTCATTCGGCGTTGCTCTGCCAGCGTGTGACGTTTGAACAGCTGCCATGGAACGCATGAAGTTTGAGAATGGACGCATCCTTGTTTCACAGGGAGAGCTGAGTGAAGGAACTTGCTGCAGAAGTTCAGTCAATCGTCGCTCCTGCCTGCGAAGATTTGCGTATTTGCGCTACAAGTGTGACCAGCCTGCTAAACTGACTGGCGAGCTGTGGCGTTAACGTCGTGGCGAAACGCGTAGCTAAGGGCAGAGAGCCAACAAGCGTACTTTGAATATCAATTACGAGCTCGTTGTTCGTACTTCATCATTCTGGGTTCGCAGAAAAGGTGACGCTTACCCCGTCGTGTGGAGTTTAGTACCTTCAGGAAAGTCACCCTGAGGATGCATAGCCGGAACTGCGTCGGAGGATCGTTTTATGACGGGGCCGTGTGTTGTTCGCCTCCATCGCGTGCTTTCGGCAATATGCACAACCTAGTCCTGGTGTTGCTGGCGTTTCTGTCTTCGTGGGAAGACAACGAAACCAGGCGCGGCGATGTGGTGGAACAGCAGAATCCTTTTCGCCTAGCGATTCACGGCAAAACTGAGAGAGACCGTGACGGGAATTGCACACAACACGGCGTGAGATCAAATGATTTCCGTTTCGTGGATGAAGGTGACATGTCTGCTGAAGTAGGTCGTGGTCTGGCTTTACAGAAACATGTCCGAGTTCCGCTGCAGGCTTCGATTGCTCGGCGGCTTTCTGACAGGGAGTCGGAAAAGAGGAGCCAAGGTTCCGACAACGGAAACGGCACTACCCCACCTTTGCCACCACGGCGGACCCCGTCTCCGCGGCCTTCAGGAGCCAGTGGAGTTGTCCAACAAGGAGCTGCCGGTGTGGGCACGCCTACGATGTTGGGGACAGGTGGCCAACATCTCTCTGACCAGGGAGCTACAGGTTCAGTCGCACCATCAGTGCAATCTTCCTCATCTAGTGCTGTCAGTGTTGAGGGTGCATTGCCTCTAATCCAGTTTTTCGGAAGCCGTAGCAGTTCTCCTGAAGTCCCTCTATGTCATGCGTGCCACACTGTAGAGGCAGCTGTAGGCGTGCTTCAAAGCATAAGACACCGCAGACGGGCTGGCGCGCGTGAGGCAGCTGAGCGAATAGCGGCACTGGAGTCCCAACATGCTCTTCTTGTCAGTTCCTCCACCCAGGGAGAGCACAGTCAAGGTGCACGGCCAAGTGATATCCTTGTGAGTCACCGGGCGCTACAACGGGCGCGCCGAGAGGCCACCCGACAGGAAGAAACGCTACGGGGAGAAGAAGCCTCCCTGGAAGCGTTTATACGCGTGGCCTCTGAAAAGCGTGAAAGAGAAGGGCAGAGGTCTCTCGAGGTGCTCCGCCAGCGCGTGGAAAATCAGACTGCAGAACTTGCTGTGTTACGCGTCGAGGCAGCACTAGAGCGGCAACGTGAAATGGTGGAGCTCGAGAGGAGGCGCGGAGACTTACTGGCCCTGGCCTTAGTCGCAGAAGACGACGAAGAATATCTTCGGCTGAGTGCAGAAGAAGAAGCAGTCCAACGGCAAATCGAGCAATTGGCGGAGGAAACGAGGAGACCGCGCCGTGGCCGTAGAAAGCCCGCGTGATGCAGAAGTGAACAGTGATTCCAAGTGTCTTAAGCACAGTTATTTGAAAAAACAACAATGCATTCTGAATGCGAAACGGTGGTATCGGAGGTATAATGTAGGTAGGGGAACGGGGCACCCCCCGATCTTATTTTGTCAGTCCTGTTACGGAAAGGAAACTGCCTTGTCGGGAGCAGAGGTAAATCCCATTAGGCGCGAGGGTAGCAGAAACCCGCTTCGTGCTGCGTTATGCTTTTGATACTCGCACGCTATTTTGATTACCTCGCAAGCACCTTTGGCGACACTGTGAAAATGCTTTTCTGACAAAGCGATACACGATTGCGGATTTCCCAGTTGGTGTCGTGGTGCGCCTGTCGCCGAATCAAGAGGACATCCTAATTGCACTTCATATGTGAATCCGGCACATACGTTCGTTACCATTTTCTCAGCAACAGGCTTCTGGAGAAACCGAAACTGGTTTTCCAGTGTAGATGGCAATGTCACTCGTGGGGATAACGAAACCCTGAAGATTGCCCTGGCGGGTTCGAAAGTATACGTTCACAGGCGTCCACCGAACATATCCTATTCATGATGTGAACAGCCTATTGATGATGTCTCTACTGAACACACTAGTTGAAAGACACCTGCGAGAGCGG
+Coding Sequence: ATGCATAGCCGGAACTGCGTCGGAGGATCGTTTTATGACGGGGCCGTGTGTTGTTCGCCTCCATCGCGTGCTTTCGGCAATATGCACAACCTAGTCCTGGTGTTGCTGGCGTTTCTGTCTTCGTGGGAAGACAACGAAACCAGGCGCGGCGATGTGGTGGAACAGCAGAATCCTTTTCGCCTAGCGATTCACGGCAAAACTGAGAGAGACCGTGACGGGAATTGCACACAACACGGCGTGAGATCAAATGATTTCCGTTTCGTGGATGAAGGTGACATGTCTGCTGAAGTAGGTCGTGGTCTGGCTTTACAGAAACATGTCCGAGTTCCGCTGCAGGCTTCGATTGCTCGGCGGCTTTCTGACAGGGAGTCGGAAAAGAGGAGCCAAGGTTCCGACAACGGAAACGGCACTACCCCACCTTTGCCACCACGGCGGACCCCGTCTCCGCGGCCTTCAGGAGCCAGTGGAGTTGTCCAACAAGGAGCTGCCGGTGTGGGCACGCCTACGATGTTGGGGACAGGTGGCCAACATCTCTCTGACCAGGGAGCTACAGGTTCAGTCGCACCATCAGTGCAATCTTCCTCATCTAGTGCTGTCAGTGTTGAGGGTGCATTGCCTCTAATCCAGTTTTTCGGAAGCCGTAGCAGTTCTCCTGAAGTCCCTCTATGTCATGCGTGCCACACTGTAGAGGCAGCTGTAGGCGTGCTTCAAAGCATAAGACACCGCAGACGGGCTGGCGCGCGTGAGGCAGCTGAGCGAATAGCGGCACTGGAGTCCCAACATGCTCTTCTTGTCAGTTCCTCCACCCAGGGAGAGCACAGTCAAGGTGCACGGCCAAGTGATATCCTTGTGAGTCACCGGGCGCTACAACGGGCGCGCCGAGAGGCCACCCGACAGGAAGAAACGCTACGGGGAGAAGAAGCCTCCCTGGAAGCGTTTATACGCGTGGCCTCTGAAAAGCGTGAAAGAGAAGGGCAGAGGTCTCTCGAGGTGCTCCGCCAGCGCGTGGAAAATCAGACTGCAGAACTTGCTGTGTTACGCGTCGAGGCAGCACTAGAGCGGCAACGTGAAATGGTGGAGCTCGAGAGGAGGCGCGGAGACTTACTGGCCCTGGCCTTAGTCGCAGAAGACGACGAAGAATATCTTCGGCTGAGTGCAGAAGAAGAAGCAGTCCAACGGCAAATCGAGCAATTGGCGGAGGAAACGAGGAGACCGCGCCGTGGCCGTAGAAAGCCCGCGTGA
+
+TABLE: SNPs Summary
+[strain_a_query]	[strain_b_query]	[Strain A]	[Strain B]	[gene_source_id]	[CDS SNP Density]	[Non-synonymous]	[Synonymous]	[Nonsense]	[Non-coding]	[Total]
+RH (type I)	VEG (type III)	RH	VEG	TGME49_000010	.81	1	0	0	4	5
+ME49 (type II)	RH (type I)	ME49	RH	TGME49_000010	.81	1	0	0	4	5
+
+TABLE: Gene Model
+[Type]	[Start]	[End]
+exon	2230843	2232576
+intron	2232577	2232920
+exon	2232921	2234577
+
+TABLE: ME49 Microarray Expression Data
+[ME49 Gene Model]
+TGME49_000010
+TGME49_045430
+
+TABLE: Three archetypal T. gondii lineages - Percentiles
+[Strain]	[Percentile]
+VEG	11.5
+CTG	23.2
+Prugniaud	71.9
+RH	78.7
+GT1	78.2
+ME49	82.7
+
+TABLE: InterPro Domains
+[Name]	[Primary ID]	[Secondary ID]	[Start Min]	[End Min]	[E-value]
+
+TABLE: Transmembrane Domains
+[Name]	[Parent ID]	[Start Min]	[End Max]	[Sequence]	[Topology]
+
+TABLE: Low Complexity Regions
+[Name]	[Parent ID]	[Start Min]	[End Max]
+263625	89354	403	410
+263623	89354	341	354
+263622	89354	287	304
+263620	89354	186	201
+263619	89354	136	166
+263621	89354	239	256
+263624	89354	367	382
+
+TABLE: Signal Peptide
+[Name]	[NN Conclusion Score]	[NN D-Score]	[HMM Signal Probabability]	[Start Min]	[End Max]
+
+TABLE: BlastP Hits
+[Feature ID]	[Name]	[Parent ID]	[Score]	[Start]	[End]	[Description]	[Expect Value]	[Percent Identity]	[Percent Positive]
+728519	TGME49_000010	89354	147	240	400	E() = 9.9e-6, 30% identity, gi|183598034|ref|ZP_02959527.1| hypothetical protein PROSTU_01390 [Providencia stuartii ATCC 25827]gi|188022813|gb|EDU60853.1| hypothetical protein PROSTU_01390 [Providencia stuartii ATCC 25827]	9.9e-6	0	0
+
+TABLE: Gene Location
+[Sequence Level]	[Genomic Sequence]	[Location]	[start]	[end]	[is_reversed]	[start_context]	[end_context]	[Feature ID]
+Chromosome	TGME49_chrXII	2230843 - 2234577 (-)	2230843	2234577	-	2225843	2239577	TGME49_000010
+Scaffold	DS984812	1393 - 5127 (+)	1393	5127	+	-3607	10127	TGME49_000010
+
+TABLE: Release 4 Genes
+[Gene ID]	[Product]	[Sequence ID]	[Location]	[=Release5 protein?]	[cyc_gene_id]	[start]	[end]	[strand]	[context_start]	[context_end]
+1.m00014	hypothetical protein	TGG_995340	1393 - 5127 (+)	Yes	1.M00014	1393	5127	+	0	10127
+
+TABLE: Notes
+[Note]
+encoded by transcript TGME49_000010A
+
+TABLE: User Comments
+[Comment ID]	[stable_id]	[comment_target_id]	[Headline]	[PubMed ID(s)]	[# Related Genes]	[# Uploaded Files]	[Made by]	[Date]
+
+TABLE: EC Number
+[EC Number]	[Source]	[EC Description]
+
+TABLE: Mass Spec.-based Expression Evidence
+[Experiment Name]	[Sequences]	[Sequence Count]	[Spectrum Count]
+
+TABLE: GO Terms
+[GO ID]	[Ontology]	[GO Term Name]	[Source]	[Evidence Code]	[lowercase_evidence_code]	[Is Not]
+
+TABLE: Orthologs and Paralogs within ToxoDB
+[Gene]	[Species]	[Product]
+TGME49_087740	Toxoplasma gondii ME49	hypothetical protein
+
+TABLE: Metabolic Pathways
+[pathway_id]	[Pathway]	[activity]
+
+TABLE: Strains summary
+[Gene]	[Strain]	[Product]	[Protein Length]	[# Exons]	[# TM]	[Signal Peptide]	[Proteomics?]	[User Comment?]
+TGME49_000010	ME49	hypothetical protein	413	2	0	No	No	Yes
+
+TABLE: Toxoplasma Genome Sequencing Project Annotation
+[TASK Annotation]
+Unsure of gene model. There is difference between the manatee and the Gbrowse gene models.<br/><b>Reviewed by</b>: DS
+
+TABLE: Antibody Reagents
+[remark]	[Reagent ID]	[Reagent Type]
+
+TABLE: External Links
+[Database]	[source_id]	[link_url]
+
+TABLE: Epitopes from IEDB
+[Epitope]	[Sequence]	[Location on Protein]	[Strain]	[Confidence]
+
+TABLE: Product
+[Product]
+hypothetical protein
+
+
+------------------------------------------------------------
+
+ID: TGME49_000110
+Gene Group: TG_16806
+Data Source: T.gondii ME49 contigs from Genbank
+Genomic Sequence ID: TGME49_chrIX
+Chromosome: IX
+Genomic Location: TGME49_chrIX: 106,477 - 106,854 (+)
+Gene Strand: forward
+Gene Type: protein coding
+# Exons: 1
+Transcript Length: 378
+CDS Length: 378
+Product Description: hypothetical protein, conserved
+Protein Length: 125
+# TM Domains: 0
+Molecular Weight: 13492
+Isoelectric Point: 5.63
+EC Numbers: null
+Ortholog count: 1
+Paralog count: 0
+Temporary Ortholog Group: ORTH_16806.tmp
+Total SNPs All Strains: 11
+Nonsynonymous SNPs All Strains: 7
+Synonymous SNPs All Strains: 4
+Nonsyn/Syn SNP Ratio All Strains: 1.75
+SignalP Scores: null
+SignalP Peptide: null
+Annotated GO Function: null
+Annotated GO Process: null
+Annotated GO Component: null
+Predicted GO Function: null
+Predicted GO Process: null
+Predicted GO Component: null
+TypeIII / TypeI fold-change: 1.01844018466976
+TypeIII / TypeII fold-change: -2.02099469638244
+TypeII / TypeI fold-change: 2.05826221180034
+Organism: Toxoplasma gondii ME49
+Release4 IDs: 2.m00067
+= Release4 Protein?: Yes
+Predicted Protein Sequence: MVLKENLRVKQVHQGEDPMDIGYQPGNVWSVGSEVDVSCCVFVERAVKPAEISGTVRECRHAPAGNSCNADCLSSPTVHVLIFLTTTTEGGVCQMAKAKYVGRRQEAICLQAALGEMLSEITNPL
+Predicted RNA/mRNA Sequence (introns spliced out): ATGGTATTAAAAGAGAATTTGCGCGTGAAGCAGGTACACCAGGGGGAGGATCCCATGGATATTGGTTACCAGCCGGGGAATGTTTGGTCCGTCGGCTCGGAGGTGGATGTGAGCTGTTGTGTATTTGTGGAACGAGCGGTGAAGCCTGCCGAAATTAGCGGAACCGTCAGAGAATGCCGCCACGCGCCTGCGGGAAACAGTTGCAACGCCGATTGTTTGTCGTCACCGACTGTGCACGTCCTTATTTTCCTCACAACGACCACCGAGGGAGGTGTTTGCCAGATGGCGAAGGCGAAGTACGTTGGCCGCCGCCAAGAAGCGATCTGTCTGCAGGCCGCCCTCGGAGAAATGCTGAGCGAGATCACAAATCCGCTATGA
+Coding Sequence: ATGGTATTAAAAGAGAATTTGCGCGTGAAGCAGGTACACCAGGGGGAGGATCCCATGGATATTGGTTACCAGCCGGGGAATGTTTGGTCCGTCGGCTCGGAGGTGGATGTGAGCTGTTGTGTATTTGTGGAACGAGCGGTGAAGCCTGCCGAAATTAGCGGAACCGTCAGAGAATGCCGCCACGCGCCTGCGGGAAACAGTTGCAACGCCGATTGTTTGTCGTCACCGACTGTGCACGTCCTTATTTTCCTCACAACGACCACCGAGGGAGGTGTTTGCCAGATGGCGAAGGCGAAGTACGTTGGCCGCCGCCAAGAAGCGATCTGTCTGCAGGCCGCCCTCGGAGAAATGCTGAGCGAGATCACAAATCCGCTATGA
+
+TABLE: SNPs Summary
+[strain_a_query]	[strain_b_query]	[Strain A]	[Strain B]	[gene_source_id]	[CDS SNP Density]	[Non-synonymous]	[Synonymous]	[Nonsense]	[Non-coding]	[Total]
+454	Me49	454	Me49	TGME49_000110	29.1	7	4	1	0	11
+
+TABLE: Gene Model
+[Type]	[Start]	[End]
+exon	106477	106854
+
+TABLE: ME49 Microarray Expression Data
+[ME49 Gene Model]
+TGME49_000110
+
+TABLE: Three archetypal T. gondii lineages - Percentiles
+[Strain]	[Percentile]
+VEG	31
+CTG	41
+ME49	51.2
+RH	32.7
+GT1	37.8
+Prugniaud	63.8
+
+TABLE: InterPro Domains
+[Name]	[Primary ID]	[Secondary ID]	[Start Min]	[End Min]	[E-value]
+
+TABLE: Transmembrane Domains
+[Name]	[Parent ID]	[Start Min]	[End Max]	[Sequence]	[Topology]
+
+TABLE: Low Complexity Regions
+[Name]	[Parent ID]	[Start Min]	[End Max]
+
+TABLE: Signal Peptide
+[Name]	[NN Conclusion Score]	[NN D-Score]	[HMM Signal Probabability]	[Start Min]	[End Max]
+
+TABLE: BlastP Hits
+[Feature ID]	[Name]	[Parent ID]	[Score]	[Start]	[End]	[Description]	[Expect Value]	[Percent Identity]	[Percent Positive]
+
+TABLE: Gene Location
+[Sequence Level]	[Genomic Sequence]	[Location]	[start]	[end]	[is_reversed]	[start_context]	[end_context]	[Feature ID]
+Chromosome	TGME49_chrIX	106477 - 106854 (+)	106477	106854	+	101477	111854	TGME49_000110
+Scaffold	DS984780	3292 - 3669 (-)	3292	3669	-	-1708	8669	TGME49_000110
+
+TABLE: Release 4 Genes
+[Gene ID]	[Product]	[Sequence ID]	[Location]	[=Release5 protein?]	[cyc_gene_id]	[start]	[end]	[strand]	[context_start]	[context_end]
+2.m00067	conserved hypothetical protein	IX	106377 - 106754 (+)	Yes	2.M00067	106377	106754	+	101377	111754
+
+TABLE: Notes
+[Note]
+encoded by transcript TGME49_000110A
+
+TABLE: User Comments
+[Comment ID]	[stable_id]	[comment_target_id]	[Headline]	[PubMed ID(s)]	[# Related Genes]	[# Uploaded Files]	[Made by]	[Date]
+
+TABLE: EC Number
+[EC Number]	[Source]	[EC Description]
+
+TABLE: Mass Spec.-based Expression Evidence
+[Experiment Name]	[Sequences]	[Sequence Count]	[Spectrum Count]
+
+TABLE: GO Terms
+[GO ID]	[Ontology]	[GO Term Name]	[Source]	[Evidence Code]	[lowercase_evidence_code]	[Is Not]
+
+TABLE: Orthologs and Paralogs within ToxoDB
+[Gene]	[Species]	[Product]	[is syntenic]	[has comments]
+
+TABLE: Metabolic Pathways
+[pathway_id]	[Pathway]	[activity]
+
+TABLE: Strains summary
+[Gene]	[Strain]	[Product]	[Protein Length]	[# Exons]	[# TM]	[Signal Peptide]	[Proteomics?]	[User Comment?]
+TGME49_000110	ME49	hypothetical protein, conserved	125	1	0	No	No	No
+
+TABLE: Toxoplasma Genome Sequencing Project Annotation
+[TASK Annotation]
+
+TABLE: Antibody Reagents
+[remark]	[Reagent ID]	[Reagent Type]
+
+TABLE: External Links
+[Database]	[source_id]	[link_url]
+
+TABLE: Epitopes from IEDB
+[Epitope]	[Sequence]	[Location on Protein]	[Strain]	[Confidence]
+
+TABLE: Product
+[Product]
+hypothetical protein, conserved
+
+
+------------------------------------------------------------
+

data/test/helper.rb

@@ -0,0 +1,9 @@
+require 'rubygems'
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+class Test::Unit::TestCase
+end

data/test/test_eupathdb_gene_information_table.rb

@@ -0,0 +1,60 @@
+
+require 'helper'
+require 'eupathdb_gene_information_table'
+
+class EuPathDBGeneInformationTableTest < Test::Unit::TestCase
+  def test_gene_splitting
+    eu = EuPathDBGeneInformationTable.new(File.open(File.join(File.dirname(__FILE__),'data','eupathGeneInformation.txt'),'r'))
+    genes = %w(TGME49_000010 TGME49_000110)
+    total = 0
+    eu.each_with_index do |info, i|
+      total += 1
+      assert_equal genes[i], info.get_info('ID')
+    end
+    assert_equal 2, total
+  end
+
+  def test_table
+    eu = EuPathDBGeneInformationTable.new(File.open(File.join(File.dirname(__FILE__),'data','eupathGeneInformation.txt'),'r'))
+    genes = [
+      {
+      'Type' => 'exon',
+      'Start' => '2230843',
+      'End' => '2232576'
+      },
+      {
+      'Type' => 'intron',
+      'Start' => '2232577',
+      'End' => '2232920'
+      },
+      {
+      'Type' => 'exon',
+      'Start' => '2232921',
+      'End' => '2234577'
+      },
+    ]
+    assert_equal genes, eu.to_a[0].get_table('Gene Model')
+  end
+
+  def test_last_entry
+    eu = EuPathDBGeneInformationTable.new(File.open(File.join(File.dirname(__FILE__),'data','eupathGeneInformation.txt'),'r'))
+    a = eu.to_a
+    first = a[0]
+    last = a[1]
+    assert_equal [{'Product' => 'hypothetical protein, conserved'}],
+      last.get_table('Product')
+    assert_equal [{'Product' => 'hypothetical protein'}],
+      first.get_table('Product')
+  end
+  
+  def test_alias_brackets
+    eu = EuPathDBGeneInformationTable.new(File.open(File.join(File.dirname(__FILE__),'data','eupathGeneInformation.txt'),'r'))
+    genes = %w(TGME49_000010 TGME49_000110)
+    total = 0
+    eu.each_with_index do |info, i|
+      total += 1
+      assert_equal genes[i], info['ID']
+    end
+    assert_equal 2, total
+  end
+end

metadata

@@ -0,0 +1,91 @@
+--- !ruby/object:Gem::Specification 
+name: reubypathdb
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-11-01 00:00:00 +11:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: thoughtbot-shoulda
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id001
+description: Classes to help parsing EuPathDB data files
+email: donttrustben near gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/eupathdb_gene_information_table.rb
+- test/data/eupathGeneInformation.txt
+- test/helper.rb
+- test/test_eupathdb_gene_information_table.rb
+has_rdoc: true
+homepage: http://github.com/wwood/reubypathdb
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: Classes to help parsing EuPathDB data files
+test_files: 
+- test/helper.rb
+- test/test_eupathdb_gene_information_table.rb