lederhosen 1.6.0 → 1.6.1

data/Gemfile

@@ -1,17 +1,16 @@
 source :rubygems
 
 gem 'dna', '0.1.2'
-gem 'progressbar'
-gem 'thor'
+gem 'progressbar', '0.12.0'
+gem 'thor', '0.16.0'
 
 group :test do
-  gem 'rspec'
-  gem 'rspec-prof'
+  gem 'rspec', '2.12.0'
+  gem 'rspec-prof', '0.0.3'
 end
 
 group :development do
   gem 'rdoc', '~> 3.12'
-  gem 'bundler'
-  gem 'jeweler'
-  gem 'ruby-prof'
+  gem 'jeweler', '1.8.4'
+  gem 'ruby-prof', '0.11.2'
 end

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.6.0"
+  s.version = "1.6.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
@@ -61,29 +61,26 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<dna>, ["= 0.1.2"])
-      s.add_runtime_dependency(%q<progressbar>, [">= 0"])
-      s.add_runtime_dependency(%q<thor>, [">= 0"])
+      s.add_runtime_dependency(%q<progressbar>, ["= 0.12.0"])
+      s.add_runtime_dependency(%q<thor>, ["= 0.16.0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<bundler>, [">= 0"])
-      s.add_development_dependency(%q<jeweler>, [">= 0"])
-      s.add_development_dependency(%q<ruby-prof>, [">= 0"])
+      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>, ["= 0.1.2"])
-      s.add_dependency(%q<progressbar>, [">= 0"])
-      s.add_dependency(%q<thor>, [">= 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<bundler>, [">= 0"])
-      s.add_dependency(%q<jeweler>, [">= 0"])
-      s.add_dependency(%q<ruby-prof>, [">= 0"])
+      s.add_dependency(%q<jeweler>, ["= 1.8.4"])
+      s.add_dependency(%q<ruby-prof>, ["= 0.11.2"])
     end
   else
     s.add_dependency(%q<dna>, ["= 0.1.2"])
-    s.add_dependency(%q<progressbar>, [">= 0"])
-    s.add_dependency(%q<thor>, [">= 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<bundler>, [">= 0"])
-    s.add_dependency(%q<jeweler>, [">= 0"])
-    s.add_dependency(%q<ruby-prof>, [">= 0"])
+    s.add_dependency(%q<jeweler>, ["= 1.8.4"])
+    s.add_dependency(%q<ruby-prof>, ["= 0.11.2"])
   end
 end
 

data/lib/lederhosen/tasks/trim.rb

@@ -46,11 +46,13 @@ module Lederhosen
         out = File.join(out_dir, "#{File.basename(prefix)}.fasta")
 
         # create the trimmed sequence generator
+        trim_args = { :pretrim => pretrim, :min_length => min_length }
+
         trimmer =
           if read_type == 'qseq'
-            Trimmer::QSEQTrimmer.new(*files)
+            Trimmer::QSEQTrimmer.new(*files, trim_args)
           elsif read_type == 'fastq'
-            Trimmer::InterleavedTrimmer.new(files)
+            Trimmer::InterleavedTrimmer.new(files, trim_args)
           end
 
         # trim and write

data/lib/lederhosen/trimmer.rb

@@ -7,6 +7,9 @@ class PairedTrimmer < Enumerator
     @paired_iterator = paired_iterator
     @pretrim         = args[:pretrim]
     @min_length      = args[:min_length] || 70
+    @min             = args[:min] || 20
+    @offset          = args[:cutoff] || 64 # XXX should both be called 'cutoff'
+    @pretrim         = args[:pretrim] || false
   end
 
   def each(&block)
@@ -38,25 +41,21 @@ class PairedTrimmer < Enumerator
   # this method does the actual trimming. It is a class method
   # so you can use it if you don't want to initialize a PairedTrimmer
   def trim_seq(dna, args={})
-    pretrim = args[:pretrim] || false
 
     # trim primers off of sequence
     # XXX this is experiment-specific and needs to be made
     # into a parameter
-    if pretrim
-      dna.sequence = dna.sequence[pretrim..-1]
-      dna.quality  = dna.quality[pretrim..-1]
+    if @pretrim
+      dna.sequence = dna.sequence[@pretrim..-1]
+      dna.quality  = dna.quality[@pretrim..-1]
     end
 
     dna.sequence.gsub! '.', 'N'
 
-    min    = args[:min]    || 20 # what is this constant?
-    offset = args[:cutoff] || 64 # XXX depends on sequencing tech.
-
     _sum, _max, first, last, start, _end = 0, 0, 0, 0, 0
 
     dna.quality.each_byte.each_with_index do |b, a|
-      _sum += (b - offset - min)
+      _sum += (b - @offset - @min)
       if _sum > _max
         _max = _sum
         _end = a

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 1
     MINOR = 6
     CODENAME = 'Sauerkraut' # changes for minor versions
-    PATCH = 0
+    PATCH = 1
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/readme.md

@@ -70,6 +70,8 @@ lederhosen cluster \
   --database=taxcollector.udb
 ```
 
+The optional `--dry-run` parameter outputs the usearch command to standard out. This is useful if you want to run usearch on a cluster.
+
 ### Generate OTU table(s)
 
 Create an OTU abundance table where rows are samples and columns are clusters. The entries are the number of reads for that cluster in a sample.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 1.6.0
+  version: 1.6.1
   prerelease: 
 platform: ruby
 authors:
@@ -32,33 +32,33 @@ dependencies:
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.12.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
-        version: '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'
+        version: 0.16.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.16.0
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
@@ -75,54 +75,38 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
-- !ruby/object:Gem::Dependency
-  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
-    none: false
-    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'
+        version: 1.8.4
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0'
+        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'
+        version: 0.11.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.11.2
 description: Various tools for OTU clustering
 email: harekrishna@gmail.com
 executables:
@@ -178,7 +162,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2684834348311279261
+      hash: -3171751151013656560
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: