lederhosen 1.8.1 → 1.8.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/lederhosen.gemspec +3 -9
- data/lib/lederhosen/tasks/otu_table.rb +3 -0
- data/lib/lederhosen/version.rb +1 -1
- data/spec/cli_spec.rb +5 -15
- data/spec/data/trimmed/ILT_L_9_B_001.fasta +1596 -0
- data/spec/no_tasks_spec.rb +19 -24
- metadata +3 -9
- data/spec/data/ILT_L_9_B_001_1.txt.gz +0 -0
- data/spec/data/ILT_L_9_B_001_3.txt.gz +0 -0
- data/spec/data/ILT_L_9_B_002_1.txt.gz +0 -0
- data/spec/data/ILT_L_9_B_002_3.txt.gz +0 -0
- data/spec/data/example.fastq +0 -400
- data/spec/data/trimmed_sizes.txt +0 -100
- data/spec/trimmer_spec.rb +0 -85
data/spec/trimmer_spec.rb
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require 'spec_helper'
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describe Lederhosen::Trimmer do
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describe Lederhosen::Trimmer::PairedTrimmer
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describe Lederhosen::Trimmer::ProbabilityTrimmer do
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let :sequence_trimmer do
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# default cutoff should be 0.005
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Lederhosen::Trimmer::ProbabilityTrimmer.new :seq_tech => :illumina
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end
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it 'can be created' do
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sequence_trimmer.should_not be_nil
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end
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it 'trims records as expected'
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end
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describe Lederhosen::Trimmer::HuangTrimmer do
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let :sequence_trimmer do
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Lederhosen::Trimmer::HuangTrimmer.new(:offset => 64, :min => 20)
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end
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it 'trims records as expected' do
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trimmed_sizes = File.readlines('spec/data/trimmed_sizes.txt').map &:to_i
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File.open('spec/data/example.fastq') do |handle|
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records = Dna.new handle
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records.each do |record|
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trimmed_record = sequence_trimmer.trim_seq record
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trimmed_record.size.should == trimmed_sizes.shift
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end
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end
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end
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end
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describe Lederhosen::Trimmer::QSEQTrimmer do
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let :qseq_trimmer do
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Lederhosen::Trimmer::QSEQTrimmer.new 'spec/data/ILT_L_9_B_001_1.txt.gz',
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'spec/data/ILT_L_9_B_001_3.txt.gz'
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end
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it 'can be initialized' do
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qseq_trimmer.should_not be_nil
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end
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it 'has an #each function that generates record objects' do
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qseq_trimmer.each do |x|
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x.should be_an_instance_of Fasta
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end
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end
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it 'should create an even number of records (not output singletons)' do
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qseq_trimmer.to_a.flatten.size.should be_even
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end
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end
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describe Lederhosen::Trimmer::InterleavedTrimmer do
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let :interleaved_trimmer do
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Lederhosen::Trimmer::InterleavedTrimmer.new 'spec/data/example.fastq'
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end
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it 'can be initialized' do
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interleaved_trimmer.should_not be_nil
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end
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it 'has an #each function that generates record objects' do
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interleaved_trimmer.each do |x|
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x.should be_an_instance_of Fasta
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end
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end
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it 'should create an even number of records (not output singletons)' do
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interleaved_trimmer.to_a.flatten.size.should be_even
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end
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end
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end
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