lederhosen 2.0.0 → 2.0.1

data/Gemfile

@@ -6,13 +6,10 @@ gem 'thor', '0.16.0'
 
 group :test do
   gem 'rspec', '2.12.0'
-  gem 'rspec-prof', '0.0.3'
   gem 'pry'
-#  gem 'plymouth'
 end
 
 group :development do
   gem 'rdoc', '~> 3.12'
   gem 'jeweler', '1.8.4'
-  gem 'ruby-prof', '0.11.2'
-end
+end

data/lederhosen.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "2.0.0"
+  s.version = "2.0.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2013-01-24"
+  s.date = "2013-01-25"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]
@@ -55,7 +55,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://audy.github.com/lederhosen"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.23"
+  s.rubygems_version = "1.8.24"
   s.summary = "OTU Clustering"
 
   if s.respond_to? :specification_version then
@@ -67,14 +67,12 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<thor>, ["= 0.16.0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<jeweler>, ["= 1.8.4"])
-      s.add_development_dependency(%q<ruby-prof>, ["= 0.11.2"])
     else
       s.add_dependency(%q<dna>, [">= 0"])
       s.add_dependency(%q<progressbar>, ["= 0.12.0"])
       s.add_dependency(%q<thor>, ["= 0.16.0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<jeweler>, ["= 1.8.4"])
-      s.add_dependency(%q<ruby-prof>, ["= 0.11.2"])
     end
   else
     s.add_dependency(%q<dna>, [">= 0"])
@@ -82,7 +80,6 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<thor>, ["= 0.16.0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<jeweler>, ["= 1.8.4"])
-    s.add_dependency(%q<ruby-prof>, ["= 0.11.2"])
   end
 end
 

data/lib/lederhosen/uc_parser.rb

@@ -14,11 +14,11 @@ module Lederhosen
     end
 
     def hit?
-      @source.type == 'H'
+      @source.hit_type == 'H'
     end
 
     def miss?
-      @source.type == 'N'
+      @source.hit_type == 'N'
     end
   end
 
@@ -63,7 +63,7 @@ module Lederhosen
       str = str.split("\t")
 
       dat = {
-        :type => str[0],
+        :hit_type => str[0],
         :cluster_no => str[1],
         :alignment => str[7],
         :query => str[8],
@@ -71,12 +71,12 @@ module Lederhosen
       }
 
       r =
-        if dat[:type] =~ /[SNH]/ # hits
+        if dat[:hit_type] =~ /[SNH]/ # hits
           { :length => str[2].to_i,
             :identity => str[3],
             :strand => str[4],
           }
-      elsif dat[:type] == 'C' # clusters
+      elsif dat[:hit_type] == 'C' # clusters
         { :cluster_size => str[2].to_i }
       else
         raise Exception, "Do not understand record type #{str[0]}!"

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 2
     MINOR = 0
     CODENAME = 'Schnittlauchbrot' # changes for minor versions
-    PATCH = 0
+    PATCH = 1
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/readme.md

@@ -13,10 +13,14 @@ Lederhosen is not a pipeline but rather a set of tools broken up into tasks. Tas
 
 Lederhosen is designed with the following "pipeline" in mind:
 
-1. Clustering sequences to centroid or reference sequences (read: database)
+1. Clustering sequences to reference sequences (read: database) and/or _de novo_ OTU clustering.
+  - `lederhosen cluster ...`
 2. Generating tables from USEARCH output.
+  - `lederhosen count_taxonomies ...`
+  - `lederhosen otu_table ...`
 3. Filtering tables to remove small or insignificant OTUs.
-4. Support for paired end reads (considers taxonomic assignment for both reads in a pair).
+  - `lederhosen otu_filter ...`
+
 
 ### About
 
@@ -33,6 +37,7 @@ using paired and non-paired end short reads such as those produced by Illumina (
 - Parallel support (pipe commands into [parallel](http://savannah.gnu.org/projects/parallel/), or use your cluster's queue).
 - Support for RDP, TaxCollector or GreenGenes 16S rRNA databases.
 - Generation and filtering of OTU abundancy matrices.
+-. Support for paired end reads (considers taxonomic assignment for both reads in a pair).
 
 ### Installation
 
@@ -169,8 +174,6 @@ for filtered clusters will be moved to the `noise` psuedocluster.
 
 ### Get representative sequences
 
-(not yet implemented)
-
 You can get the representative sequences for each cluster using the `get_reps` tasks.
 This will extract the representative sequence from the __database__ you ran usearch with.
 Make sure you use the same database that you used when running usearch.

data/spec/cli_spec.rb

@@ -33,11 +33,11 @@ describe Lederhosen::CLI do
   it 'can separate unclassified reads from usearch output' do
     `./bin/lederhosen separate_unclassified --uc-file=spec/data/test.uc --reads=spec/data/trimmed/ILT_L_9_B_001.fasta --output=#{$test_dir}/unclassified.fasta`
     $?.success?.should be_true
-    unclassified_results = File.readlines("spec/data/test.uc")
-                               .select { |x| x =~ /^N/ }
+    unclassified_results = File.readlines("spec/data/test.uc")\
+                               .select { |x| x =~ /^N/ }\
                                .size
-    unclassified_reads = File.readlines("#{$test_dir}/unclassified.fasta")
-                             .select { |x| x =~ /^>/ }
+    unclassified_reads = File.readlines("#{$test_dir}/unclassified.fasta")\
+                             .select { |x| x =~ /^>/ }\
                              .size
   
     unclassified_results.should == unclassified_reads
@@ -46,8 +46,8 @@ describe Lederhosen::CLI do
   it 'can separate unclassified reads from usearch output using strict pairing' do
     `./bin/lederhosen separate_unclassified --strict=genus --uc-file=spec/data/test.uc --reads=spec/data/trimmed/ILT_L_9_B_001.fasta --output=#{$test_dir}/unclassified.strict_genus.fasta`
     $?.success?.should be_true
-    File.readlines("#{$test_dir}/unclassified.strict_genus.fasta")
-      .select { |x| x =~ /^>/ }
+    File.readlines("#{$test_dir}/unclassified.strict_genus.fasta")\
+      .select { |x| x =~ /^>/ }\
       .size.should be_even
   end
 
@@ -58,10 +58,10 @@ describe Lederhosen::CLI do
   end
 
   it 'generates taxonomy tables w/ comma-free taxonomic descriptions' do
-    File.readlines(File.join($test_dir, 'taxonomy_count.txt'))
-      .map(&:strip)
-      .map { |x| x.count(',') }
-      .uniq
+    File.readlines(File.join($test_dir, 'taxonomy_count.txt'))\
+      .map(&:strip)\
+      .map { |x| x.count(',') }\
+      .uniq\
       .should == [1]
   end
 
@@ -74,11 +74,11 @@ describe Lederhosen::CLI do
 
       # make sure total number of reads is even
       # requires that there should be an odd number if classification is not strict
-      lines.select { |x| !(x =~ /^#/) }
-           .map(&:strip)
-           .map { |x| x.split(',') }
-           .map(&:last)
-           .map(&:to_i)
+      lines.select { |x| !(x =~ /^#/) }\
+           .map(&:strip)\
+           .map { |x| x.split(',') }\
+           .map(&:last)\
+           .map(&:to_i)\
            .inject(:+).should be_even
     end
   end

metadata

@@ -1,120 +1,108 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: lederhosen
-version: !ruby/object:Gem::Version
-  version: 2.0.0
+version: !ruby/object:Gem::Version 
+  hash: 13
   prerelease: 
+  segments: 
+  - 2
+  - 0
+  - 1
+  version: 2.0.1
 platform: ruby
-authors:
+authors: 
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-24 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: dna
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
+
+date: 2013-01-25 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: progressbar
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.12.0
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
   type: :runtime
+  name: dna
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - "="
+      - !ruby/object:Gem::Version 
+        hash: 47
+        segments: 
+        - 0
+        - 12
+        - 0
         version: 0.12.0
-- !ruby/object:Gem::Dependency
-  name: thor
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.16.0
   type: :runtime
+  name: progressbar
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - "="
+      - !ruby/object:Gem::Version 
+        hash: 95
+        segments: 
+        - 0
+        - 16
+        - 0
         version: 0.16.0
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
-  type: :development
+  type: :runtime
+  name: thor
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 1.8.4
+      - !ruby/object:Gem::Version 
+        hash: 31
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
   type: :development
+  name: rdoc
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - "="
+      - !ruby/object:Gem::Version 
+        hash: 63
+        segments: 
+        - 1
+        - 8
+        - 4
         version: 1.8.4
-- !ruby/object:Gem::Dependency
-  name: ruby-prof
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.11.2
   type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.11.2
+  name: jeweler
+  version_requirements: *id005
 description: Various tools for OTU clustering
 email: harekrishna@gmail.com
-executables:
+executables: 
 - lederhosen
 extensions: []
-extra_rdoc_files:
+
+extra_rdoc_files: 
 - LICENSE.txt
-files:
+files: 
 - .rspec
 - Gemfile
 - LICENSE.txt
@@ -150,31 +138,37 @@ files:
 - spec/spec_helper.rb
 - spec/uc_parser_spec.rb
 homepage: http://audy.github.com/lederhosen
-licenses:
+licenses: 
 - MIT
 post_install_message: 
 rdoc_options: []
-require_paths:
+
+require_paths: 
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement
+required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
-      segments:
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
       - 0
-      hash: -4054085501911268272
-required_rubygems_version: !ruby/object:Gem::Requirement
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
 requirements: []
+
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: OTU Clustering
 test_files: []
+