lederhosen 0.2.12 → 0.2.13

data/.rspec

@@ -1 +1 @@
--c
+-c --fail-fast

data/Gemfile

@@ -12,5 +12,4 @@ group :development do
   gem 'rdoc', '~> 3.12'
   gem 'bundler'
   gem 'jeweler'
-  gem 'rcov'
 end

data/Rakefile

@@ -34,14 +34,6 @@ Rake::TestTask.new(:test) do |test|
   test.verbose = true
 end
 
-require 'rcov/rcovtask'
-Rcov::RcovTask.new do |test|
-  test.libs << 'test'
-  test.pattern = 'test/**/test_*.rb'
-  test.verbose = true
-  test.rcov_opts << '--exclude "gems/*"'
-end
-
 task :default => :test
 
 require 'rdoc/task'

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "0.2.12"
+  s.version = "0.2.13"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
@@ -71,7 +71,6 @@ Gem::Specification.new do |s|
       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<rcov>, [">= 0"])
     else
       s.add_dependency(%q<dna>, [">= 0"])
       s.add_dependency(%q<progressbar>, [">= 0"])
@@ -79,7 +78,6 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, [">= 0"])
       s.add_dependency(%q<jeweler>, [">= 0"])
-      s.add_dependency(%q<rcov>, [">= 0"])
     end
   else
     s.add_dependency(%q<dna>, [">= 0"])
@@ -88,7 +86,6 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, [">= 0"])
     s.add_dependency(%q<jeweler>, [">= 0"])
-    s.add_dependency(%q<rcov>, [">= 0"])
   end
 end
 

data/lib/lederhosen/tasks/uc_filter.rb

@@ -23,10 +23,12 @@ module Lederhosen
       ohai "filtering #{input} to #{output}, reads = #{reads} & samples = #{samples}"
 
       # load UC file
+      ohai "loading uc file"
       clstr_info   = Helpers.load_uc_file input
       clstr_counts = clstr_info[:clstr_counts] # clstr_counts[:clstr][sample.to_i] = reads
 
       # filter
+      ohai "filtering"
       survivors = clstr_counts.reject do |a, b|
         b.reject{ |i, j| j < reads }.length < samples
       end
@@ -34,13 +36,18 @@ module Lederhosen
       surviving_clusters = survivors.keys.to_set
 
       # print filtered uc file
+      ohai "saving filtered table"
       out = File.open(output, 'w')
-      kept, total = 1, 0
+
       lines = `wc -l #{input}`.split.first.to_i
+
       pbar = ProgressBar.new 'saving', lines
+      kept, total = 1, 0
+
       File.open(input) do |handle|
         handle.each do |line|
           pbar.inc
+
           if line =~ /^#/
             out.print line
             next
@@ -48,15 +55,18 @@ module Lederhosen
 
           total += 1
 
+          # check if cluster is in surviving clusters
           if surviving_clusters.include? line.split[1].to_i
             out.print line
             kept += 1
           end
+
         end
       end
+
       pbar.finish
       out.close
-      ohai "Survivors"
+
       ohai "clusters: #{surviving_clusters.length}/#{clstr_counts.keys.length} = #{100*surviving_clusters.length/clstr_counts.keys.length.to_f}%"
       ohai "reads:    #{kept}/#{total} = #{100*kept/total.to_f}%"
     end

data/lib/lederhosen/version.rb

@@ -2,7 +2,7 @@ module Lederhosen
   module Version
     MAJOR = 0
     MINOR = 2
-    PATCH = 12
+    PATCH = 13
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/spec/cli_spec.rb

@@ -54,7 +54,13 @@ describe Lederhosen::CLI do
   it 'should identify clusters given a taxcollector database'
 
   it 'should add names to otu abundance matrix given blat output' do
-    level = %w{kingdom domain phylum class order genus speces}.choice
+    levels = %w{kingdom domain phylum class order genus speces}
+    level =
+      begin
+        levels.sample # 1.9 and up
+      rescue
+        levels.choice # 1.8 and lower
+      end
     `./bin/lederhosen add_names --table=spec/data/otus.csv --blat=spec/data/blat.txt --level=#{level} --output=#{$test_dir}/named_otus.csv`
     $?.success?.should be_true
   end

data/spec/helpers_spec.rb

@@ -21,6 +21,6 @@ describe Lederhosen::Helpers do
     reads = groups.values.first
     Lederhosen::Helpers.trim_pairs reads[0], reads[1], "#{$test_dir}/munchen_trim_test.fasta"
     # this test will break if trim parameters change
-    File.read("#{$test_dir}/munchen_trim_test.fasta").grep(/^>/).length.should be_even
+    File.readlines("#{$test_dir}/munchen_trim_test.fasta").grep(/^>/).length.should be_even
   end
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 15
+  hash: 13
   prerelease: 
   segments: 
   - 0
   - 2
-  - 12
-  version: 0.2.12
+  - 13
+  version: 0.2.13
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -102,20 +102,6 @@ dependencies:
   version_requirements: *id006
   name: jeweler
   prerelease: false
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id007 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id007
-  name: rcov
-  prerelease: false
 description: Various tools for OTU clustering
 email: harekrishna@gmail.com
 executables: