def testProcessForwardDataset(self):
args.truncate = None
args.paired = False
args.forward_fastq = 'test/test1.fastq'
args.reverse_fastq = None
args.output_prefix = 'test/test_output/forward'
args.output_compression = 'none'
moira.main(args)
self.assertEqual(
open('test/test_output/forward.qc.good.fasta').read(),
open('test/test_results/forward.qc.good.fasta').read())
self.assertEqual(
open('test/test_output/forward.qc.good.qual').read(),
open('test/test_results/forward.qc.good.qual').read())
self.assertEqual(
open('test/test_output/forward.qc.good.names').read(),
open('test/test_results/forward.qc.good.names').read())
self.assertEqual(
open('test/test_output/forward.qc.bad.fasta').read(),
open('test/test_results/forward.qc.bad.fasta').read())
self.assertEqual(
open('test/test_output/forward.qc.bad.qual').read(),
open('test/test_results/forward.qc.bad.qual').read())
self.assertEqual(
open('test/test_output/forward.qc.bad.names').read(),
open('test/test_results/forward.qc.bad.names').read())
def testCompression(self):
args.truncate = None
args.paired = True
args.forward_fastq = 'test/test1.fastq.gz'
args.reverse_fastq = 'test/test2.fastq.bz2'
args.output_prefix = 'test/test_output/paired'
args.output_compression = 'gz'
moira.main(args)
self.assertEqual(gzip.GzipFile('test/test_output/paired.qc.good.fasta.gz').read(), open('test/test_results/paired.qc.good.fasta').read())
args.output_compression = 'bz2'
moira.main(args)
self.assertEqual(bz2.BZ2File('test/test_output/paired.qc.good.fasta.bz2').read(), open('test/test_results/paired.qc.good.fasta').read())
def testProcessPairedDataset(self):
args.truncate = None
args.paired = True
args.forward_fastq = 'test/test1.fastq'
args.reverse_fastq = 'test/test2.fastq'
args.output_prefix = 'test/test_output/paired'
args.output_compression = 'none'
moira.main(args)
self.assertEqual(open('test/test_output/paired.qc.good.fasta').read(), open('test/test_results/paired.qc.good.fasta').read())
self.assertEqual(open('test/test_output/paired.qc.good.qual').read(), open('test/test_results/paired.qc.good.qual').read())
self.assertEqual(open('test/test_output/paired.qc.good.names').read(), open('test/test_results/paired.qc.good.names').read())
self.assertEqual(open('test/test_output/paired.qc.bad.fasta').read(), open('test/test_results/paired.qc.bad.fasta').read())
self.assertEqual(open('test/test_output/paired.qc.bad.qual').read(), open('test/test_results/paired.qc.bad.qual').read())
self.assertEqual(open('test/test_output/paired.qc.bad.names').read(), open('test/test_results/paired.qc.bad.names').read())
def testCompression(self):
args.truncate = None
args.paired = True
args.forward_fastq = 'test/test1.fastq.gz'
args.reverse_fastq = 'test/test2.fastq.bz2'
args.output_prefix = 'test/test_output/paired'
args.output_compression = 'gz'
moira.main(args)
self.assertEqual(
gzip.GzipFile('test/test_output/paired.qc.good.fasta.gz').read(),
open('test/test_results/paired.qc.good.fasta').read())
args.output_compression = 'bz2'
moira.main(args)
self.assertEqual(
bz2.BZ2File('test/test_output/paired.qc.good.fasta.bz2').read(),
open('test/test_results/paired.qc.good.fasta').read())
