lederhosen 0.3.3 → 0.3.4

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "0.3.3"
+  s.version = "0.3.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
@@ -40,6 +40,7 @@ Gem::Specification.new do |s|
     "lib/lederhosen/tasks/rep_reads.rb",
     "lib/lederhosen/tasks/sort.rb",
     "lib/lederhosen/tasks/split.rb",
+    "lib/lederhosen/tasks/split_fasta.rb",
     "lib/lederhosen/tasks/squish.rb",
     "lib/lederhosen/tasks/trim.rb",
     "lib/lederhosen/tasks/uc_filter.rb",

data/lib/lederhosen/tasks/split_fasta.rb

@@ -0,0 +1,33 @@
+##
+# Split a fasta file into many fasta files with n reads
+#
+
+module Lederhosen
+  class CLI
+
+    desc 'split_fasta',
+      'splits input fasta file into separate fasta files containing n reads'
+
+    method_option :input,   :type => :string,  :required => true
+    method_option :out_dir, :type => :string,  :required => true
+    method_option :n,       :type => :numeric, :required => true
+
+    def split_fasta
+      input   = options[:input]
+      out_dir = options[:out_dir]
+      n       = options[:n].to_i
+
+      ohai "splitting #{input} into files with #{n} reads stored in #{out_dir}"
+
+      `mkdir -p #{out_dir}`
+
+      File.open input do |handle|
+        Dna.new(handle).each_with_index do |record, i|
+          @out = File.open(File.join(out_dir, "split_#{i/n}.fasta"), 'w') if i%n == 0
+          @out.puts record
+        end
+      end
+
+    end
+  end
+end

data/lib/lederhosen/version.rb

@@ -2,7 +2,7 @@ module Lederhosen
   module Version
     MAJOR = 0
     MINOR = 3
-    PATCH = 3
+    PATCH = 4
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

metadata

@@ -1,120 +1,118 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: lederhosen
-version: !ruby/object:Gem::Version
-  version: 0.3.3
+version: !ruby/object:Gem::Version 
+  hash: 27
   prerelease: 
+  segments: 
+  - 0
+  - 3
+  - 4
+  version: 0.3.4
 platform: ruby
-authors:
+authors: 
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-14 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: dna
-  requirement: !ruby/object:Gem::Requirement
+
+date: 2012-08-14 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  type: :runtime
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - "="
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 0
+        - 0
+        - 12
         version: 0.0.12
-  type: :runtime
+  version_requirements: *id001
+  name: dna
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+- !ruby/object:Gem::Dependency 
+  type: :runtime
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.0.12
-- !ruby/object:Gem::Dependency
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id002
   name: progressbar
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+- !ruby/object:Gem::Dependency 
+  type: :runtime
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id003
   name: thor
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
-  type: :development
+      - !ruby/object:Gem::Version 
+        hash: 31
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
+  version_requirements: *id004
+  name: rdoc
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
-- !ruby/object:Gem::Dependency
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id005
   name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id006
   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
@@ -138,6 +136,7 @@ files:
 - lib/lederhosen/tasks/rep_reads.rb
 - lib/lederhosen/tasks/sort.rb
 - lib/lederhosen/tasks/split.rb
+- lib/lederhosen/tasks/split_fasta.rb
 - lib/lederhosen/tasks/squish.rb
 - lib/lederhosen/tasks/trim.rb
 - lib/lederhosen/tasks/uc_filter.rb
@@ -157,31 +156,37 @@ 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
-      version: '0'
-      segments:
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
       - 0
-      hash: 1714359518753916587
-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: 1.8.24
 signing_key: 
 specification_version: 3
 summary: OTU Clustering
 test_files: []
+