lederhosen 0.3.2 → 0.3.3

data/bin/lederhosen

@@ -2,6 +2,4 @@
 
 require File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib', 'lederhosen'))
 
-fail "you need to install uclust and have it in your $PATH" if `which uclust` == ''
-
 Lederhosen::CLI.start

data/lederhosen.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "0.3.2"
+  s.version = "0.3.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2012-08-13"
+  s.date = "2012-08-14"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]

data/lib/lederhosen/cli.rb

@@ -1,4 +1,8 @@
 module Lederhosen
+
+  ##
+  # The CLI class holds all of the Thor tasks
+  #
   class CLI < Thor
     include Thor::Actions
 

data/lib/lederhosen/helpers.rb

@@ -109,10 +109,20 @@ module Lederhosen
           clusternr   = line[1].to_i
           querylabel  = line[8]
           targetlabel = line[9]
-          sample      = line[8].split(':')[2]
+          header      = line[8]
+
+          # get the sample id via regexp match
+          # this way more info can be stored in the header.
+          sample = line[8].match(/sample=(.*)/)[1]
+
+          # Need to maintain some backwards compatibility here
+          # this is the old way of getting the same id.
+          if sample.nil?
+            sample = line[8].split(':')[2]
+          end
 
           # keep track of samples
-          samples.add sample
+          samples.add(sample)
 
           # keep track of all samples
           clusters[:samples].add sample

data/lib/lederhosen/tasks/join.rb

@@ -33,7 +33,7 @@ module Lederhosen
         end
 
         records.each_slice(2) do |l, r|
-          output.puts ">#{r.name}:#{File.basename(fasta_file, '.fasta')}\n#{r.sequence.reverse+l.sequence}"
+          output.puts ">#{r.name}:split=#{r.sequence.size}:sample=#{File.basename(fasta_file, '.fasta')}\n#{r.sequence.reverse+l.sequence}"
         end
       end
       pbar.finish

data/lib/lederhosen/version.rb

@@ -2,7 +2,7 @@ module Lederhosen
   module Version
     MAJOR = 0
     MINOR = 3
-    PATCH = 2
+    PATCH = 3
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/lib/lederhosen.rb

@@ -7,6 +7,11 @@ require 'set'
 
 Dir.glob(File.join(File.dirname(__FILE__), 'lederhosen', '*.rb')).each { |f| require f }
 
+##
+# Here I extend the string class to add the to_kmers method
+#
+# Does it really need to be a method of String? Sure, why not?
+#
 class String
   def to_kmers(k)
     return [] if k == 0

metadata

@@ -1,118 +1,120 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: lederhosen
-version: !ruby/object:Gem::Version 
-  hash: 23
+version: !ruby/object:Gem::Version
+  version: 0.3.3
   prerelease: 
-  segments: 
-  - 0
-  - 3
-  - 2
-  version: 0.3.2
 platform: ruby
-authors: 
+authors:
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-08-13 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  type: :runtime
-  requirement: &id001 !ruby/object:Gem::Requirement 
+date: 2012-08-14 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: dna
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - "="
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 0
-        - 0
-        - 12
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
         version: 0.0.12
-  version_requirements: *id001
-  name: dna
-  prerelease: false
-- !ruby/object:Gem::Dependency 
   type: :runtime
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id002
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.0.12
+- !ruby/object:Gem::Dependency
   name: progressbar
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id003
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: thor
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
   prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 3
-        - 12
-        version: "3.12"
-  version_requirements: *id004
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: rdoc
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
   type: :development
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id005
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
   name: bundler
-  prerelease: false
-- !ruby/object:Gem::Dependency 
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id006
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
   name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
   prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 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
 - .rvmrc
 - Gemfile
@@ -155,37 +157,31 @@ files:
 - spec/misc_spec.rb
 - spec/spec_helper.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 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: 1714359518753916587
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: OTU Clustering
 test_files: []
-