lederhosen 1.8.1 → 1.8.2

data/lederhosen.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.8.1"
+  s.version = "1.8.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
@@ -43,16 +43,10 @@ Gem::Specification.new do |s|
     "scripts/otu_ref_picking/readme.md",
     "scripts/readme.md",
     "spec/cli_spec.rb",
-    "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/example.fastq",
     "spec/data/test.uc",
-    "spec/data/trimmed_sizes.txt",
+    "spec/data/trimmed/ILT_L_9_B_001.fasta",
     "spec/no_tasks_spec.rb",
-    "spec/spec_helper.rb",
-    "spec/trimmer_spec.rb"
+    "spec/spec_helper.rb"
   ]
   s.homepage = "http://audy.github.com/lederhosen"
   s.licenses = ["MIT"]

data/lib/lederhosen/tasks/otu_table.rb

@@ -54,6 +54,9 @@ module Lederhosen
                 else
                   dat[level] || 'unparsed_name'
                 end
+              
+              # remove commas from name
+              name = name.tr(',', '_')
 
               # the next two lines are what is slow
               level_sample_cluster_count[level][input_file][name] += 1

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 1
     MINOR = 8
     CODENAME = 'Karottensaft' # changes for minor versions
-    PATCH = 1
+    PATCH = 2
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/spec/cli_spec.rb

@@ -12,30 +12,20 @@ describe Lederhosen::CLI do
     $?.success?.should be_true
   end
 
-  it 'should trim paired QSEQ reads' do
-    `./bin/lederhosen trim --reads-dir=spec/data/IL*.txt.gz --out-dir=#{$test_dir}/trimmed`
-    $?.success?.should be_true
-  end
-
-  it 'should trim paired, interleaved FASTQ reads' do
-    `./bin/lederhosen trim --reads-dir=spec/data/example.fastq --out-dir=#{$test_dir}/trimmed --read-type fastq`
-    $?.success?.should be_true
-  end
-
   it 'can create a usearch udb using usearch' do
-    `./bin/lederhosen make_udb --input #{$test_dir}/trimmed/ILT_L_9_B_001.fasta --output #{$test_dir}/test_db.udb`
+    `./bin/lederhosen make_udb --input spec/data/trimmed/ILT_L_9_B_001.fasta --output #{$test_dir}/test_db.udb`
     $?.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 #{$test_dir}/clusters.uc`
+    stdout = `./bin/lederhosen cluster --dry-run --input spec/data/trimmed/ILT_L_9_B_001.fasta --database #{$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 #{$test_dir}/clusters.uc`
+    `./bin/lederhosen cluster --input spec/data/trimmed/ILT_L_9_B_001.fasta --database #{$test_dir}/test_db.udb --identity 0.95 --output #{$test_dir}/clusters.uc`
     $?.success?.should be_true
     File.exists?(File.join($test_dir, 'clusters.uc')).should be_true
   end
@@ -57,12 +47,12 @@ describe Lederhosen::CLI do
   end
 
   it 'should split a fasta file into smaller fasta files (optionally gzipped)' do
-    `./bin/lederhosen split_fasta --input=#{$test_dir}/trimmed/ILT_L_9_B_001.fasta --out-dir=#{$test_dir}/split/ --gzip true -n 100`
+    `./bin/lederhosen split_fasta --input=spec/data/trimmed/ILT_L_9_B_001.fasta --out-dir=#{$test_dir}/split/ --gzip true -n 100`
     $?.success?.should be_true
   end
 
   it 'should print representative sequences from uc files' do
-    `./bin/lederhosen get_reps --input=#{$test_dir}/clusters.uc --database=#{$test_dir}/trimmed/ILT_L_9_B_001.fasta --output=#{$test_dir}/representatives.fasta`
+    `./bin/lederhosen get_reps --input=#{$test_dir}/clusters.uc --database=spec/data/trimmed/ILT_L_9_B_001.fasta --output=#{$test_dir}/representatives.fasta`
   end
 
   it 'should create a fasta file containing representative reads for each cluster'