Sha256: 10a5a695228de1024b9c6ec4f9cec6b33de7c9cf707ed566f31627109ffd5288
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Versions: 16
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Stored size: 1.28 KB
Contents
test_dir = "/tmp/lederhosen_test_#{(0...8).map{65.+(rand(25)).chr}.join}/"
`mkdir -p #{test_dir}`
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/*.txt --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
end
Version data entries
16 entries across 16 versions & 1 rubygems