lederhosen 1.3.4 → 1.3.5
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- data/lederhosen.gemspec +2 -2
- data/lib/lederhosen/no_tasks.rb +15 -1
- data/lib/lederhosen/version.rb +1 -1
- data/spec/no_tasks_spec.rb +8 -2
- metadata +3 -3
data/lederhosen.gemspec
CHANGED
@@ -5,11 +5,11 @@
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5
5
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6
6
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Gem::Specification.new do |s|
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7
7
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s.name = "lederhosen"
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8
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-
s.version = "1.3.
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8
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+
s.version = "1.3.5"
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9
9
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10
10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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11
11
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s.authors = ["Austin G. Davis-Richardson"]
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12
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-
s.date = "2012-12-
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12
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+
s.date = "2012-12-04"
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13
13
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s.description = "Various tools for OTU clustering"
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14
14
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s.email = "harekrishna@gmail.com"
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15
15
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s.executables = ["lederhosen"]
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data/lib/lederhosen/no_tasks.rb
CHANGED
@@ -76,6 +76,13 @@ module Lederhosen
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76
76
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77
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# parse a taxonomic description using the
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78
78
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# taxcollector format returning name at each level (genus, etc...)
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79
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+
#
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80
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+
# - If the species names contains the word '_bacterium', use the strain
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81
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+
# name as the species name:
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82
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+
#
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83
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+
# Escherichia_bacterium -> Escherichia_bacterium_strain_X123
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84
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+
# Arcanobacterium_phocae -> Arcanobacterium_phocae (no change)
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85
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+
#
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79
86
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def parse_taxonomy_taxcollector(taxonomy)
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80
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81
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levels = { 'domain' => 0,
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@@ -85,7 +92,8 @@ module Lederhosen
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'order' => 3,
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'family' => 4,
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94
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'genus' => 5,
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88
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-
'species' => 6
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95
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+
'species' => 6,
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96
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+
'strain' => 7 }
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89
97
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98
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names = Hash.new
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91
99
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@@ -94,6 +102,12 @@ module Lederhosen
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94
102
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names[level] = name
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95
103
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end
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96
104
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105
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+
# check if species name contains the word 'bacterium'
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106
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+
# if so, replace it with the strain name
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107
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+
if names['species'] =~ /_bacterium/
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108
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+
names['species'] = names['strain']
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109
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+
end
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110
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+
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97
111
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# keep original taxonomic description
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98
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names['original'] = taxonomy
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99
113
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data/lib/lederhosen/version.rb
CHANGED
data/spec/no_tasks_spec.rb
CHANGED
@@ -6,7 +6,7 @@ describe 'no_tasks' do
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6
6
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7
7
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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',
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8
8
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'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Rahnella;s__' ]}
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9
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-
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'] }
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9
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+
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'] }
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10
10
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it '#detect_taxonomy_format should recognize GreenGenes' do
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greengenes_taxonomies.each do |greengenes_taxonomy|
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@@ -29,7 +29,7 @@ describe 'no_tasks' do
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29
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taxonomy = lederhosen.parse_taxonomy_taxcollector(taxcollector_taxonomy)
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taxonomy['original'].should == taxcollector_taxonomy
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31
31
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32
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-
levels = %w{domain phylum class order family genus species kingdom original}
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32
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+
levels = %w{domain phylum class order family genus species kingdom original strain}
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33
33
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34
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taxonomy.keys.each do |v|
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levels.should include v
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@@ -59,4 +59,10 @@ describe 'no_tasks' do
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59
59
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lederhosen.parse_taxonomy(taxcollector_taxonomy).should_not be_nil
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60
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end
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61
61
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end
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62
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+
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63
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+
it '#parse_taxonomy_taxcollector should replace unclassified species names with strain name' do
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64
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t = '[0]Bacteria;[1]Actinobacteria;[2]Actinobacteria;[3]Actinomycetales;[4]test;[5]null;[6]Propionibacterineae_bacterium;[7]Propionibacterineae_bacterium_870BRRJ;[8]Propionibacterineae_bacterium_870BRRJ|genus'
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65
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tax = lederhosen.parse_taxonomy(t)
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66
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tax['species'].should == tax['strain']
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67
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end
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62
68
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end
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: lederhosen
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3
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version: !ruby/object:Gem::Version
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4
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-
version: 1.3.
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4
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+
version: 1.3.5
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5
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prerelease:
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6
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platform: ruby
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7
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authors:
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@@ -9,7 +9,7 @@ authors:
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9
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autorequire:
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10
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bindir: bin
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11
11
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cert_chain: []
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12
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-
date: 2012-12-
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12
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+
date: 2012-12-04 00:00:00.000000000 Z
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13
13
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dependencies:
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14
14
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- !ruby/object:Gem::Dependency
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name: dna
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@@ -160,7 +160,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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160
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version: '0'
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161
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segments:
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162
162
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- 0
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163
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-
hash:
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163
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+
hash: 502535867079393177
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164
164
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required_rubygems_version: !ruby/object:Gem::Requirement
|
165
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none: false
|
166
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requirements:
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