lederhosen 0.1.6 → 0.1.7

data/spec/pipeline_spec.rb

@@ -1,8 +1,4 @@
-test_dir = "/tmp/lederhosen_test_#{(0...8).map{65.+(rand(25)).chr}.join}/"
-
-`mkdir -p #{test_dir}`
-
-$stderr.puts "test dir: #{test_dir}"; sleep 1
+require 'spec_helper'
 
 describe 'the pipeline' do
 
@@ -12,44 +8,44 @@ describe 'the pipeline' do
   end
 
   it 'should trim reads' do
-    `./bin/lederhosen trim --reads-dir=spec/data/IL*.txt --out-dir=#{test_dir}/trimmed`
+    `./bin/lederhosen trim --reads-dir=spec/data/IL*.txt.gz --out-dir=#{$test_dir}/trimmed`
     $?.success?.should be_true
   end
 
   it 'should join reads' do
-    `./bin/lederhosen join --trimmed=#{test_dir}/trimmed/*.fasta --output=#{test_dir}/joined.fasta`
+    `./bin/lederhosen join --trimmed=#{$test_dir}/trimmed/*.fasta --output=#{$test_dir}/joined.fasta`
     $?.success?.should be_true
   end
 
   it 'should sort reads' do
-    `./bin/lederhosen sort --input=#{test_dir}/joined.fasta --output=#{test_dir}/sorted.fasta`
+    `./bin/lederhosen sort --input=#{$test_dir}/joined.fasta --output=#{$test_dir}/sorted.fasta`
     $?.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=#{$test_dir}/sorted.fasta --output=#{$test_dir}/clusters.uc`
     $?.success?.should be_true
   end
 
   it 'should build OTU abundance matrices' do
-    `./bin/lederhosen otu_table --clusters=#{test_dir}/clusters.uc --output=#{test_dir}/test_tables --joined=#{test_dir}/joined.fasta`
+    `./bin/lederhosen otu_table --clusters=#{$test_dir}/clusters.uc --output=#{$test_dir}/test_tables --joined=#{$test_dir}/joined.fasta`
     $?.success?.should be_true
   end
 
   it 'should split joined.fasta into reads for each cluster' do
-    `./bin/lederhosen split --reads=#{test_dir}/joined.fasta --clusters=#{test_dir}/clusters.uc --out-dir=#{test_dir}/split --min-clst-size=1`
+    `./bin/lederhosen split --reads=#{$test_dir}/joined.fasta --clusters=#{$test_dir}/clusters.uc --out-dir=#{$test_dir}/split --min-clst-size=1`
   end
 
-	it 'should name 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
-    `./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
+  it 'should name clusters given a taxcollector database'
 
-	it 'should squish otu abundance matrix by same name' do
-		`./bin/lederhosen squish --csv-file=#{test_dir}/named_otus.csv --output=#{test_dir}/squished.csv"`
-		$?.success?.should be_true
-	end
+  it 'should add names to otu abundance matrix given blat output' do
+    level = %w{kingdom domain phylum class order genus speces}.choice
+    `./bin/lederhosen add_names --table=spec/data/otus.csv --blat=spec/data/blat.txt --level=#{level} --output=#{$test_dir}/named_otus.csv`
+    $?.success?.should be_true
+  end
+
+  it 'should squish otu abundance matrix by same name' do
+    `./bin/lederhosen squish --csv-file=#{$test_dir}/named_otus.csv --output=#{$test_dir}/squished.csv`
+    $?.success?.should be_true
+  end
 end

data/spec/spec_helper.rb

@@ -1,2 +1,6 @@
 $:.unshift File.join(File.dirname(__FILE__), '..')
-require 'lederhosen'
+require 'lederhosen'
+
+$test_dir = ENV['TEST_DIR'] || "/tmp/lederhosen_test_#{(0...8).map{65.+(rand(25)).chr}.join}/"
+`mkdir -p #{$test_dir}`
+$stderr.puts "test dir: #{$test_dir}"

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 23
+  hash: 21
   prerelease: 
   segments: 
   - 0
   - 1
-  - 6
-  version: 0.1.6
+  - 7
+  version: 0.1.7
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-07-16 00:00:00 Z
+date: 2012-07-17 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: dna
@@ -129,6 +129,7 @@ files:
 - .rvmrc
 - Gemfile
 - bin/lederhosen
+- examples/hierarchical_clustering.sh
 - examples/pipeline.sh
 - lederhosen.gemspec
 - lib/lederhosen.rb
@@ -150,12 +151,10 @@ files:
 - lib/lederhosen/tasks/uc_filter.rb
 - lib/version.rb
 - readme.md
-- spec/data/ILT_L_9_B_001_1.txt
-- spec/data/ILT_L_9_B_001_3.txt
-- spec/data/ILT_L_9_B_002_1.txt
-- spec/data/ILT_L_9_B_002_3.txt
-- spec/data/blast_out.txt
-- spec/data/blat.txt
+- spec/data/ILT_L_9_B_001_1.txt.gz
+- spec/data/ILT_L_9_B_001_3.txt.gz
+- spec/data/ILT_L_9_B_002_1.txt.gz
+- spec/data/ILT_L_9_B_002_3.txt.gz
 - spec/data/otus.csv
 - spec/helpers_spec.rb
 - spec/misc_spec.rb
@@ -195,12 +194,10 @@ signing_key:
 specification_version: 3
 summary: 16S rRNA clustering for paired-end Illumina
 test_files: 
-- spec/data/ILT_L_9_B_001_1.txt
-- spec/data/ILT_L_9_B_001_3.txt
-- spec/data/ILT_L_9_B_002_1.txt
-- spec/data/ILT_L_9_B_002_3.txt
-- spec/data/blast_out.txt
-- spec/data/blat.txt
+- spec/data/ILT_L_9_B_001_1.txt.gz
+- spec/data/ILT_L_9_B_001_3.txt.gz
+- spec/data/ILT_L_9_B_002_1.txt.gz
+- spec/data/ILT_L_9_B_002_3.txt.gz
 - spec/data/otus.csv
 - spec/helpers_spec.rb
 - spec/misc_spec.rb