def test_summary_not_demultiplexed_gzipped_no_header(self):
artifact_type = 'SFF'
filepaths = {'raw_sff': [join(dirname(__file__), 'test_data',
'Fasting_Example.sff.gz')]}
obs = _summary_not_demultiplexed(artifact_type, filepaths)
exp = ["<h3>Fasting_Example.sff.gz (raw_sff)</h3>",
"<b>MD5:</b>: 2b636ee4833270da41a39aa5fc0a1622</br>"]
self.assertEqual(obs, exp)
def test_summary_not_demultiplexed_not_gzipped_header(self):
test_dir = mkdtemp()
self._clean_up_files.append(test_dir)
bcds_fp = join(test_dir, 'barcodes.fastq')
with open(bcds_fp, 'w') as fh:
fh.write(BARCODES)
fwd_fp = join(test_dir, 'reads.fastq')
with open(fwd_fp, 'w') as fh:
fh.write(READS)
artifact_type = 'FASTQ'
filepaths = {'raw_forward_seqs': [fwd_fp],
'raw_barcodes': [bcds_fp]}
obs = _summary_not_demultiplexed(artifact_type, filepaths)
exp = [
'<h3>barcodes.fastq (raw_barcodes)</h3>',
'<b>MD5:</b>: d0478899bf5c6ba6019b596690e8c261</br>',
'<p style="font-family:\'Courier New\', Courier, monospace;'
'font-size:10;">@MISEQ03:123:000000000-A40KM:1:1101:14149:1572 '
'1:N:0:TCCACAGGAGT\n<br/>TCCACAGGAGT\n<br/>+\n<br/>CCCCCCCCCFF\n'
'<br/>@MISEQ03:123:000000000-A40KM:1:1101:14170:1596 1:N:0:'
'TCCACAGGAGT\n<br/>TCCACAGGAGT\n<br/>+\n<br/>CCCCCCCCCCF\n<br/>@'
'MISEQ03:123:000000000-A40KM:1:1101:14740:1607 1:N:0:TCCACAGGAGT\n'
'<br/>TCCACAGGAGT\n</p><hr/>',
'<h3>reads.fastq (raw_forward_seqs)</h3>',
'<b>MD5:</b>: 97328e860ef506f7b029997b12bf9885</br>',
'<p style="font-family:\'Courier New\', Courier, monospace;'
'font-size:10;">@MISEQ03:123:000000000-A40KM:1:1101:14149:1572 '
'1:N:0:TCCACAGGAGT\n<br/>GGGGGGTGCCAGCCGCCGCGGTAATACGGGGGGGGCAAGCG'
'TTGTTCGGAATTACTGGGCGTAAAGGGCTCGTAGGCGGCCCACTAAGTCAGACGTGAAATCCCTC'
'GGCTTAACCGGGGAACTGCGTCTGATACTGGATGGCTTGAGGTTGGGAGAGGGATGCGGAATTCC'
'AGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACC'
'AATTCTGACGCTGAG\n<br/>+\n<br/>CCCCCCCCCFFFGGGGGGGGGGGGHHHHGGGGGFF'
'FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-.;FFFFFFFFF9@EFFFF'
'FFFFFFFFFFFFFFF9CFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFECF'
'FFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFF;CDEA@FFFFF'
'FFFFFFFFFFFFFFFFFFFFF\n<br/>@MISEQ03:123:000000000-A40KM:1:1101:1'
'4170:1596 1:N:0:TCCACAGGAGT\n<br/>ATGGCGTGCCAGCAGCCGCGGTAATACGGAG'
'GGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTGTAAGTTAGAGGT'
'GAAAGCCCGGGGCTCAACTCCGGAACTGCCTTTAAGACTGCATCGCTAGAATTGTGGAGAGGTGA'
'GTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCAGTGGCGAAGGCGAC'
'TCACTGGACACATATTGACGCTGAG\n<br/>+\n<br/>CCCCCCCCCCFFGGGGGGGGGGGGG'
'HHHGGGGGGGGGHHHGGGGGHHGGGGGHHHHHHHHGGGGHHHGGGGGHHHGHGGGGGHHHHHHHH'
'GHGHHHHHHGHHHHGGGGGGHHHHHHHGGGGGHHHHHHHHHGGFGGGGGGGGGGGGGGGGGGGGG'
'GGGFGGFFFFFFFFFFFFFFFFFF0BFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFF'
'FDFAFCFFFFFFFFFFFFFFFFFFBDFFFFF\n<br/>@MISEQ03:123:000000000-A40K'
'M:1:1101:14740:1607 1:N:0:TCCACAGGAGT\n<br/>AGTGTGTGCCAGCAGCCGCGG'
'TAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTCGTTG'
'TGTCTGCTGTGAAATCCCCGGGCTCAACCTGGGAATGGCAGTGGAAACTGGCGAGCTTGAGTGTG'
'GCAGAGGGGGGGGGAATTCCGCGTGTAGCAGTGAAATGCGTAGAGATGCGGAGGAACACCGATGG'
'CGAAGGCAACCCCCTGGGATAATATTTACGCTCAT\n</p><hr/>']
self.assertItemsEqual(obs, exp)
def test_summary_not_demultiplexed_gzipped_header(self):
test_dir = mkdtemp()
self._clean_up_files.append(test_dir)
bcds_fp = join(test_dir, 'barcodes.fastq.gz')
with GzipFile(bcds_fp, mode='w', mtime=1) as fh:
fh.write(BARCODES)
fwd_fp = join(test_dir, 'reads.fastq.gz')
with GzipFile(fwd_fp, mode='w', mtime=1) as fh:
fh.write(READS)
artifact_type = 'FASTQ'
filepaths = {'raw_forward_seqs': [fwd_fp],
'raw_barcodes': [bcds_fp]}
obs = _summary_not_demultiplexed(artifact_type, filepaths)
exp = [
'<h3>barcodes.fastq.gz (raw_barcodes)</h3>',
'<b>MD5:</b>: 1c6eefa11d8641a6f853b56801351e5a</br>',
'<p style="font-family:\'Courier New\', Courier, monospace;'
'font-size:10;">@MISEQ03:123:000000000-A40KM:1:1101:14149:1572 '
'1:N:0:TCCACAGGAGT\n<br/>TCCACAGGAGT\n<br/>+\n<br/>CCCCCCCCCFF\n'
'<br/>@MISEQ03:123:000000000-A40KM:1:1101:14170:1596 1:N:0:'
'TCCACAGGAGT\n<br/>TCCACAGGAGT\n<br/>+\n<br/>CCCCCCCCCCF\n<br/>@'
'MISEQ03:123:000000000-A40KM:1:1101:14740:1607 1:N:0:TCCACAGGAGT\n'
'<br/>TCCACAGGAGT\n</p><hr/>',
'<h3>reads.fastq.gz (raw_forward_seqs)</h3>',
'<b>MD5:</b>: f3909bcab34565a5d4b88c300d40bbfc</br>',
'<p style="font-family:\'Courier New\', Courier, monospace;'
'font-size:10;">@MISEQ03:123:000000000-A40KM:1:1101:14149:1572 '
'1:N:0:TCCACAGGAGT\n<br/>GGGGGGTGCCAGCCGCCGCGGTAATACGGGGGGGGCAAGCG'
'TTGTTCGGAATTACTGGGCGTAAAGGGCTCGTAGGCGGCCCACTAAGTCAGACGTGAAATCCCTC'
'GGCTTAACCGGGGAACTGCGTCTGATACTGGATGGCTTGAGGTTGGGAGAGGGATGCGGAATTCC'
'AGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACC'
'AATTCTGACGCTGAG\n<br/>+\n<br/>CCCCCCCCCFFFGGGGGGGGGGGGHHHHGGGGGFF'
'FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-.;FFFFFFFFF9@EFFFF'
'FFFFFFFFFFFFFFF9CFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFECF'
'FFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFF;CDEA@FFFFF'
'FFFFFFFFFFFFFFFFFFFFF\n<br/>@MISEQ03:123:000000000-A40KM:1:1101:1'
'4170:1596 1:N:0:TCCACAGGAGT\n<br/>ATGGCGTGCCAGCAGCCGCGGTAATACGGAG'
'GGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTGTAAGTTAGAGGT'
'GAAAGCCCGGGGCTCAACTCCGGAACTGCCTTTAAGACTGCATCGCTAGAATTGTGGAGAGGTGA'
'GTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCAGTGGCGAAGGCGAC'
'TCACTGGACACATATTGACGCTGAG\n<br/>+\n<br/>CCCCCCCCCCFFGGGGGGGGGGGGG'
'HHHGGGGGGGGGHHHGGGGGHHGGGGGHHHHHHHHGGGGHHHGGGGGHHHGHGGGGGHHHHHHHH'
'GHGHHHHHHGHHHHGGGGGGHHHHHHHGGGGGHHHHHHHHHGGFGGGGGGGGGGGGGGGGGGGGG'
'GGGFGGFFFFFFFFFFFFFFFFFF0BFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFF'
'FDFAFCFFFFFFFFFFFFFFFFFFBDFFFFF\n<br/>@MISEQ03:123:000000000-A40K'
'M:1:1101:14740:1607 1:N:0:TCCACAGGAGT\n<br/>AGTGTGTGCCAGCAGCCGCGG'
'TAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTCGTTG'
'TGTCTGCTGTGAAATCCCCGGGCTCAACCTGGGAATGGCAGTGGAAACTGGCGAGCTTGAGTGTG'
'GCAGAGGGGGGGGGAATTCCGCGTGTAGCAGTGAAATGCGTAGAGATGCGGAGGAACACCGATGG'
'CGAAGGCAACCCCCTGGGATAATATTTACGCTCAT\n</p><hr/>']
self.assertItemsEqual(obs, exp)
def test_summary_not_demultiplexed_empty(self):
test_dir = mkdtemp()
self._clean_up_files.append(test_dir)
fwd_fp = join(test_dir, 'reads.fastq')
open(fwd_fp, 'w', 0).close()
artifact_type = 'per_sample_FASTQ'
filepaths = {'preprocessed_fastq': [fwd_fp]}
obs = _summary_not_demultiplexed(artifact_type, filepaths)
exp = [
'<h3>reads.fastq (preprocessed_fastq)</h3>',
'<b>MD5:</b>: d41d8cd98f00b204e9800998ecf8427e</br>']
self.assertItemsEqual(obs, exp)