Contents

require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
require 'bio-commandeer'

#Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm')

describe "FinishM explore" do
  it 'should explore just a single but rather complex trail' do
    data_path = File.join(TEST_DATA_DIR,'explore','1')
    trails = nil
    Dir.chdir(data_path) do
      trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} explore --quiet --contigs a.fa --interesting-ends random:end --output-explored-paths - --fasta 2seqs.sammy.fa"
    end
    splits = trails.split("\n").to_a.sort
    splits.length.should == 1024
    splits[0].match(/>random:end Dead end \/ coverage nodes:(\d),[\d,]+/)[1].should == '1'
    splits[1023][0...100].should == 'CCTATCCGGTCCCCCTAGAATGTTGATTCCTCCGTCTTCTGATTTCCGTTGGCGGTTCGTATCGGCTCCCGTACAACCGCCGGAATTGAAGTGTACCTTG'
  end

  it 'should explore when interesting ends is all' do
    data_path = File.join(TEST_DATA_DIR,'explore','1')
    trails = nil
    Dir.chdir(data_path) do
      trails = Bio::Commandeer.run "#{FINISHM_SCRIPT_PATH} explore --quiet --contigs a.fa --interesting-ends all --output-explored-paths - --fasta 2seqs.sammy.fa"
    end
    splits = trails.split("\n").to_a
    splits.length.should == 1026
    splits[0].match(/>random:start Dead end \/ coverage nodes:(\d)/)[1].should == '1'
  end
end

Version data entries

8 entries across 8 versions & 1 rubygems

Version	Path
finishm-0.0.9	spec/explore_spec.rb
finishm-0.0.8	spec/explore_spec.rb
finishm-0.0.7	spec/explore_spec.rb
finishm-0.0.6	spec/explore_spec.rb
finishm-0.0.5	spec/explore_spec.rb
finishm-0.0.4	spec/explore_spec.rb
finishm-0.0.2	spec/explore_spec.rb
finishm-0.0.1	spec/explore_spec.rb