lederhosen 0.2.0 → 0.2.1

data/lib/lederhosen/tasks/k_filter.rb

@@ -23,14 +23,18 @@ module Lederhosen
       total_reads = 0
 
       ohai "counting kmers"
+      total_reads = `grep -c '^>' #{input}`.strip.split.first.to_i
+      pbar = ProgressBar.new 'count kmers', total_reads.to_i
       File.open(input) do |handle|
         records = Dna.new handle
         records.each do |r|
+          pbar.inc
           total_reads += 1
           kmers = r.sequence.to_kmers(k_len)
           kmers.each { |x| counting_table[x] += 1 }
         end
       end
+      pbar.finish
 
       sum_of_kmers = counting_table.values.inject(:+)
 
@@ -65,7 +69,7 @@ module Lederhosen
             kept += 1
             output.puts r
           end
-          pbar.inc      
+          pbar.inc
         end
       end
 

data/lib/version.rb

@@ -1,3 +1,3 @@
 module Lederhosen
-  VERSION = '0.2.0'
+  VERSION = '0.2.1'
 end

data/spec/pipeline_spec.rb

@@ -22,8 +22,13 @@ describe 'the pipeline' do
     $?.success?.should be_true
   end
 
+  it 'should k_filter reads' do
+    `./bin/lederhosen k_filter --input=#{$test_dir}/sorted.fasta --output=#{$test_dir}/filtered.fasta -k=15 --cutoff 1`
+    $?.success?.should be_true
+  end
+
   it 'should cluster reads' do
-    `./bin/lederhosen cluster --identity=0.80 --input=#{$test_dir}/sorted.fasta --output=#{$test_dir}/clusters.uc`
+    `./bin/lederhosen cluster --identity=0.80 --input=#{$test_dir}/filtered.fasta --output=#{$test_dir}/clusters.uc`
     $?.success?.should be_true
   end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 23
+  hash: 21
   prerelease: 
   segments: 
   - 0
   - 2
-  - 0
-  version: 0.2.0
+  - 1
+  version: 0.2.1
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-07-26 00:00:00 Z
+date: 2012-07-30 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: dna