Contents

require 'spec_helper'

describe 'the pipeline' do

  it 'should exist' do
    `./bin/lederhosen`
    $?.success?.should be_true
  end

  it 'should trim reads' do
    `./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`
    $?.success?.should be_true
  end

  it 'should sort reads' do
    `./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`
    $?.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`
    $?.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`
  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 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

Version data entries

4 entries across 4 versions & 1 rubygems

Version	Path
lederhosen-0.2.0	spec/pipeline_spec.rb
lederhosen-0.1.9	spec/pipeline_spec.rb
lederhosen-0.1.8	spec/pipeline_spec.rb
lederhosen-0.1.7	spec/pipeline_spec.rb