lederhosen 1.3.3 → 1.3.4

data/lederhosen.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.3.3"
+  s.version = "1.3.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2012-11-26"
+  s.date = "2012-12-03"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]

data/lib/lederhosen/no_tasks.rb

@@ -28,14 +28,13 @@ module Lederhosen
       #
       # - :taxcollector
       # - :greengenes
-      # 
+      #
       def detect_taxonomy_format(taxonomy)
-        # greengenes has a number as the first item in the header
-        # so let's just go with that
-        if taxonomy.split.first =~ /^[\d*]/
-          :greengenes
-        else
+        # taxcollector taxonomy starts with a open square bracked
+        if taxonomy =~ /^\[/
           :taxcollector
+        else
+          :greengenes
         end
       end
 

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 1
     MINOR = 3
     CODENAME = 'Dirndl' # changes for minor versions
-    PATCH = 3
+    PATCH = 4
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/spec/no_tasks_spec.rb

@@ -4,15 +4,20 @@ lederhosen = Lederhosen::CLI.new
 
 describe 'no_tasks' do
 
-  let(:greengenes_taxonomy) { '124 U55236.1 Methanobrevibacter thaueri str. CW k__Archaea; p__Euryarchaeota; c__Methanobacteria; o__Methanobacteriales; f__Methanobacteriaceae; g__Methanobrevibacter; Unclassified; otu_127' }
-  let(:taxcollector_taxonomy) { '[0]Bacteria;[1]Actinobacteria;[2]Actinobacteria;[3]null;[4]null;[5]null;[6]bacterium_TH3;[7]bacterium_TH3;[8]bacterium_TH3|M79434|8 ' } 
+  let(:greengenes_taxonomies) { ['124 U55236.1 Methanobrevibacter thaueri str. CW k__Archaea; p__Euryarchaeota; c__Methanobacteria; o__Methanobacteriales; f__Methanobacteriaceae; g__Methanobrevibacter; Unclassified; otu_127',
+                                 'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Rahnella;s__' ]}
+  let(:taxcollector_taxonomies) { ['[0]Bacteria;[1]Actinobacteria;[2]Actinobacteria;[3]null;[4]null;[5]null;[6]bacterium_TH3;[7]bacterium_TH3;[8]bacterium_TH3|M79434|8'] } 
 
   it '#detect_taxonomy_format should recognize GreenGenes' do
-    lederhosen.detect_taxonomy_format(greengenes_taxonomy).should == :greengenes
+    greengenes_taxonomies.each do |greengenes_taxonomy|
+      lederhosen.detect_taxonomy_format(greengenes_taxonomy).should == :greengenes
+    end
   end
 
   it '#detect_taxonomy_format should recognize TaxCollector' do
-    lederhosen.detect_taxonomy_format(taxcollector_taxonomy).should == :taxcollector
+    taxcollector_taxonomies.each do |taxcollector_taxonomy|
+      lederhosen.detect_taxonomy_format(taxcollector_taxonomy).should == :taxcollector
+    end
   end
 
   it '#detect_taxonomy_format should fail on unknown formats' do
@@ -20,30 +25,38 @@ describe 'no_tasks' do
   end
 
   it '#parse_taxonomy_taxcollector should parse taxcollector taxonomy' do
-    taxonomy = lederhosen.parse_taxonomy_taxcollector(taxcollector_taxonomy)
-    taxonomy['original'].should == taxcollector_taxonomy
-    
-    levels = %w{domain phylum class order family genus species kingdom original}
+    taxcollector_taxonomies.each do |taxcollector_taxonomy|
+      taxonomy = lederhosen.parse_taxonomy_taxcollector(taxcollector_taxonomy)
+      taxonomy['original'].should == taxcollector_taxonomy
+
+      levels = %w{domain phylum class order family genus species kingdom original}
 
-    taxonomy.keys.each do |v|
-      levels.should include v
+      taxonomy.keys.each do |v|
+        levels.should include v
+      end
     end
   end
 
   it '#parse_taxonomy_greengenes should parse greengenes taxonomy' do
-    taxonomy = lederhosen.parse_taxonomy_greengenes(greengenes_taxonomy)
-    levels = %w{domain phylum class order family genus species kingdom original}
+    greengenes_taxonomies.each do |greengenes_taxonomy|
+      taxonomy = lederhosen.parse_taxonomy_greengenes(greengenes_taxonomy)
+      levels = %w{domain phylum class order family genus species kingdom original}
 
-    taxonomy.keys.each do |v|
-      levels.should include v
+      taxonomy.keys.each do |v|
+        levels.should include v
+      end
     end
   end
 
   it '#parse_taxonomy should automatically detect and parse greengenes taxonomy' do
-    lederhosen.parse_taxonomy(greengenes_taxonomy).should_not be_nil
+    greengenes_taxonomies.each do |greengenes_taxonomy|
+      lederhosen.parse_taxonomy(greengenes_taxonomy).should_not be_nil
+    end
   end
 
   it '#parse_taxonomy should automatically detect and parse taxcollector taxonomy' do
-    lederhosen.parse_taxonomy(taxcollector_taxonomy).should_not be_nil
+    taxcollector_taxonomies.each do |taxcollector_taxonomy|
+      lederhosen.parse_taxonomy(taxcollector_taxonomy).should_not be_nil
+    end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 1.3.3
+  version: 1.3.4
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-26 00:00:00.000000000 Z
+date: 2012-12-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dna
@@ -160,7 +160,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 154104254980930156
+      hash: 2143498304454718392
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: