Contents

require 'spec_helper'

describe Lederhosen::CLI do

  it 'should have an executable' do
    `./bin/lederhosen`
    $?.success?.should be_true
  end

  it 'should have a version command' do
    `./bin/lederhosen version `.strip.should == "lederhosen-#{Lederhosen::Version::STRING}"
    $?.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 '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`
    $?.success?.should be_true
  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`
  end

  %w{domain phylum class ORDER Family genus species}.each do |level|
    it "should build #{level} abundance matrix" do
      `./bin/lederhosen otu_table --files=spec/data/test.uc --output=#{$test_dir}/otu_table.csv --level=#{level}`
      $?.success?.should be_true
    end
  end

  it 'should filter OTU abundance matrices' do
    `./bin/lederhosen otu_filter --input=#{$test_dir}/otu_table.csv --output=#{$test_dir}/otu_table.filtered.csv --reads 1 --samples 1`
    $?.success?.should be_true
  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`
    $?.success?.should be_true
  end

  it 'should create a fasta file containing representative reads for each cluster'
end

Version data entries

2 entries across 2 versions & 1 rubygems

Version	Path
lederhosen-1.0.1	spec/cli_spec.rb
lederhosen-1.0.0	spec/cli_spec.rb