lederhosen 1.2.5 → 1.3.0

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.2.5"
+  s.version = "1.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
@@ -45,6 +45,7 @@ Gem::Specification.new do |s|
     "spec/data/ILT_L_9_B_002_3.txt.gz",
     "spec/data/test.uc",
     "spec/misc_spec.rb",
+    "spec/no_tasks_spec.rb",
     "spec/spec_helper.rb"
   ]
   s.homepage = "http://audy.github.com/lederhosen"

data/lib/lederhosen/no_tasks.rb

@@ -23,9 +23,61 @@ module Lederhosen
         { :identity => identity }.merge(taxonomies)
       end
 
+      # detect whether the taxonomy is one of the following
+      # possible formats:
+      #
+      # - :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
+        end
+      end
+
+      def parse_taxonomy(taxonomy)
+        format = detect_taxonomy_format(taxonomy)
+
+        case format
+        when :greengenes
+          parse_taxonomy_greengenes(taxonomy)
+        when :taxcollector
+          parse_taxonomy_taxcollector(taxonomy)
+        else
+          fail 'unknown format!'
+        end
+      end
+
+      def parse_taxonomy_greengenes(taxonomy)
+
+        levels = { 'domain'  => /k__(\w*)/,
+                   'kingdom' => /k__(\w*)/,
+                   'phylum'  => /p__(\w*)/,
+                   'class'   => /c__(\w*)/,
+                   'order'   => /o__(\w*)/,
+                   'family'  => /f__(\w*)/,
+                   'genus'   => /g__(\w*)/,
+                   'species' => /s__(\w*)/
+                  }
+
+        names = Hash.new
+
+        levels.each_pair do |level, regexp|
+          names[level] = taxonomy.match(regexp)[1] rescue nil
+        end
+
+        names['original'] = taxonomy
+
+        names
+      end
+
       # parse a taxonomic description using the
       # taxcollector format returning name at each level (genus, etc...)
-      def parse_taxonomy(taxonomy)
+      def parse_taxonomy_taxcollector(taxonomy)
 
         levels = { 'domain'  => 0,
                    'kingdom' => 0,
@@ -44,7 +96,7 @@ module Lederhosen
         end
 
         # keep original taxonomic description
-        names[:original] = taxonomy
+        names['original'] = taxonomy
 
         names
       end

data/lib/lederhosen/tasks/get_reps.rb

@@ -26,7 +26,7 @@ module Lederhosen
           pbar.inc
           handle.each do |line|
             header = parse_usearch_line(line.strip)
-            taxa << header[:original] rescue nil
+            taxa << header['original'] rescue nil
           end
         end
       end

data/lib/lederhosen/version.rb

@@ -1,9 +1,9 @@
 module Lederhosen
   module Version
     MAJOR = 1
-    MINOR = 2
-    CODENAME = 'Regenmantel' # changes for minor versions
-    PATCH = 5
+    MINOR = 3
+    CODENAME = 'Dirndl' # changes for minor versions
+    PATCH = 0
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/spec/no_tasks_spec.rb

@@ -0,0 +1,49 @@
+require 'spec_helper'
+
+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 ' } 
+
+  it '#detect_taxonomy_format should recognize GreenGenes' do
+    lederhosen.detect_taxonomy_format(greengenes_taxonomy).should == :greengenes
+  end
+
+  it '#detect_taxonomy_format should recognize TaxCollector' do
+    lederhosen.detect_taxonomy_format(taxcollector_taxonomy).should == :taxcollector
+  end
+
+  it '#detect_taxonomy_format should fail on unknown formats' do
+    lederhosen.detect_taxonomy_format('this is not a taxonomic description').should raise_error
+  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}
+
+    taxonomy.keys.each do |v|
+      levels.should include v
+    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}
+
+    taxonomy.keys.each do |v|
+      levels.should include v
+    end
+  end
+
+  it '#parse_taxonomy should automatically detect and parse greengenes taxonomy' do
+    lederhosen.parse_taxonomy(greengenes_taxonomy).should_not be_nil
+  end
+
+  it '#parse_taxonomy should automatically detect and parse taxcollector taxonomy' do
+    lederhosen.parse_taxonomy(taxcollector_taxonomy).should_not be_nil
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 1.2.5
+  version: 1.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -143,6 +143,7 @@ files:
 - spec/data/ILT_L_9_B_002_3.txt.gz
 - spec/data/test.uc
 - spec/misc_spec.rb
+- spec/no_tasks_spec.rb
 - spec/spec_helper.rb
 homepage: http://audy.github.com/lederhosen
 licenses:
@@ -159,7 +160,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -656727926212445001
+      hash: -3539547832258076669
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: