lederhosen 1.3.10 → 1.4.0

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.3.10"
+  s.version = "1.4.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]

data/lib/lederhosen/tasks/cluster.rb

@@ -10,6 +10,7 @@ module Lederhosen
     method_option :identity, :type => :numeric, :required => true
     method_option :output,   :type => :string,  :required => true
     method_option :strand,   :type => :string,  :default => 'plus'
+    method_option :dry_run,  :type => :boolean, :default => false
 
     def cluster
       input    = File.expand_path(options[:input])
@@ -18,8 +19,9 @@ module Lederhosen
       identity = options[:identity]
       output   = File.expand_path(options[:output])
       strand   = options[:strand]
+      dry_run  = options[:dry_run]
 
-      ohai "clustering #{input} to #{database} and saving to #{output}"
+      ohai "#{'(dry run)' if dry_run} clustering #{input} to #{database} and saving to #{output}"
 
       options.each_pair do |key, value|
         ohai "#{key} = #{value}"
@@ -40,7 +42,11 @@ module Lederhosen
 
       cmd = cmd.join(' ')
 
-      run cmd
+      unless dry_run
+        run cmd
+      else
+        puts cmd
+      end
     end
   end
 end

data/lib/lederhosen/version.rb

@@ -1,9 +1,9 @@
 module Lederhosen
   module Version
     MAJOR = 1
-    MINOR = 3
-    CODENAME = 'Dirndl' # changes for minor versions
-    PATCH = 10
+    MINOR = 4
+    CODENAME = 'Strickjacke' # changes for minor versions
+    PATCH = 0
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/spec/cli_spec.rb

@@ -22,6 +22,13 @@ describe Lederhosen::CLI do
     $?.success?.should be_true
   end
 
+  it 'can (dry run) cluster reads using usearch and output usearch cmd to stdout' do
+    stdout = `./bin/lederhosen cluster --dry-run --input #{$test_dir}/trimmed/ILT_L_9_B_001.fasta --database #{$test_dir}/test_db.udb --identity 0.95 --output #{$test_dir}/clusters.uc`
+    stdout.should match /^usearch/
+    $?.success?.should be_true
+    File.exists?(File.join($test_dir, 'clusters.uc')).should be_false
+  end
+
   it 'can cluster reads using usearch' do
     `./bin/lederhosen cluster --input #{$test_dir}/trimmed/ILT_L_9_B_001.fasta --database #{$test_dir}/test_db.udb --identity 0.95 --output #{$test_dir}/clusters.uc`
     $?.success?.should be_true

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 1.3.10
+  version: 1.4.0
   prerelease: 
 platform: ruby
 authors:
@@ -176,7 +176,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2999187278262571353
+      hash: 598176715743028608
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: