def test_sequence_length_uses_subsample_paired(self):
random.seed(6) # Will select s1 and s2 which aren't the shortest pairs
forward = [('@s1/1 abc/1', 'GGG', '+', 'YYY'),
('@s2/1 abc/1', 'CCCCC', '+', 'PPPPP'),
('@s3/1 abc/1', 'A', '+', 'P'),
('@s4/1 abc/1', 'TTTTTTT', '+', 'PPPPPPP')]
reverse = [('@s1/1 abc/1', 'AAAAA', '+', 'YYYYY'),
('@s2/1 abc/1', 'TTTTTTT', '+', 'PPPPPPP'),
('@s3/1 abc/1', 'GGG', '+', 'PPP'),
('@s4/1 abc/1', 'C', '+', 'P')]
bpsi = BarcodePairedSequenceFastqIterator(self.barcodes, forward,
reverse)
barcode_map = pd.Series(['AAAA', 'AACC'],
name='bc',
index=pd.Index(['sample1', 'sample2'],
name='id'))
barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
demux_data = emp_paired(bpsi, barcode_map)
with tempfile.TemporaryDirectory() as output_dir:
summarize(output_dir, _PlotQualView(demux_data, paired=True), n=2)
plot_fp = os.path.join(output_dir, 'data.jsonp')
with open(plot_fp, 'r') as fh:
jsonp = fh.read()
json_ = jsonp.replace('app.init(', '[').replace(');', ']')
payload = json.loads(json_)[0]
self.assertEqual(payload["minSeqLen"]["forward"], 3)
self.assertEqual(payload["minSeqLen"]["reverse"], 5)
def test_paired_end(self):
barcodes = self.barcodes[:3]
forward = self.sequences[:3]
reverse = [('@s1/1 abc/1', 'CCC', '+', 'YYY'),
('@s2/1 abc/1', 'GGG', '+', 'PPP'),
('@s3/1 abc/1', 'TTT', '+', 'PPP')]
bpsi = BarcodePairedSequenceFastqIterator(barcodes, forward, reverse)
barcode_map = pd.Series(['AAAA', 'AACC', 'TTAA'],
name='bc',
index=pd.Index(
['sample1', 'sample2', 'sample3'],
name='id'))
barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
demux_data = emp_paired(bpsi, barcode_map)
with tempfile.TemporaryDirectory() as output_dir:
result = summarize(output_dir,
_PlotQualView(demux_data, paired=True),
n=2)
self.assertTrue(result is None)
plot_fp = os.path.join(output_dir, 'quality-plot.html')
with open(plot_fp, 'r') as fh:
html = fh.read()
self.assertIn('<h5 class="text-center">Forward Reads</h5>',
html)
self.assertIn('<h5 class="text-center">Reverse Reads</h5>',
html)
def test_rev_comp_barcodes(self):
barcodes = [('@s1/2 abc/2', 'TTTT', '+', 'YYYY'),
('@s2/2 abc/2', 'TTAA', '+', 'PPPP'),
('@s3/2 abc/2', 'GGTT', '+', 'PPPP'),
('@s4/2 abc/2', 'TTAA', '+', 'PPPP'),
('@s5/2 abc/2', 'GGTT', '+', 'PPPP'),
('@s6/2 abc/2', 'TTTT', '+', 'PPPP'),
('@s7/2 abc/2', 'GCCG', '+', 'PPPP'),
('@s8/2 abc/2', 'TTCC', '+', 'PPPP'),
('@s9/2 abc/2', 'GCCG', '+', 'PPPP'),
('@s10/2 abc/2', 'GCCG', '+', 'PPPP'),
('@s11/2 abc/2', 'TTCC', '+', 'PPPP')]
bpsi = BarcodePairedSequenceFastqIterator(barcodes, self.forward,
self.reverse)
self.check_valid(bpsi, self.barcode_map, rev_comp_barcodes=True)
def setUp(self):
self.barcodes = [('@s1/2 abc/2', 'AAAA', '+', 'YYYY'),
('@s2/2 abc/2', 'TTAA', '+', 'PPPP'),
('@s3/2 abc/2', 'AACC', '+', 'PPPP'),
('@s4/2 abc/2', 'TTAA', '+', 'PPPP'),
('@s5/2 abc/2', 'AACC', '+', 'PPPP'),
('@s6/2 abc/2', 'AAAA', '+', 'PPPP'),
('@s7/2 abc/2', 'CGGC', '+', 'PPPP'),
('@s8/2 abc/2', 'GGAA', '+', 'PPPP'),
('@s9/2 abc/2', 'CGGC', '+', 'PPPP'),
('@s10/2 abc/2', 'CGGC', '+', 'PPPP'),
('@s11/2 abc/2', 'GGAA', '+', 'PPPP')]
self.forward = [('@s1/1 abc/1', 'GGG', '+', 'YYY'),
('@s2/1 abc/1', 'CCC', '+', 'PPP'),
('@s3/1 abc/1', 'AAA', '+', 'PPP'),
('@s4/1 abc/1', 'TTT', '+', 'PPP'),
('@s5/1 abc/1', 'ATA', '+', 'PPP'),
('@s6/1 abc/1', 'TAT', '+', 'PPP'),
('@s7/1 abc/1', 'CGC', '+', 'PPP'),
('@s8/1 abc/1', 'GCG', '+', 'PPP'),
('@s9/1 abc/1', 'ACG', '+', 'PPP'),
('@s10/1 abc/1', 'GCA', '+', 'PPP'),
('@s11/1 abc/1', 'TGA', '+', 'PPP')]
self.reverse = [('@s1/1 abc/1', 'CCC', '+', 'YYY'),
('@s2/1 abc/1', 'GGG', '+', 'PPP'),
('@s3/1 abc/1', 'TTT', '+', 'PPP'),
('@s4/1 abc/1', 'AAA', '+', 'PPP'),
('@s5/1 abc/1', 'TAT', '+', 'PPP'),
('@s6/1 abc/1', 'ATA', '+', 'PPP'),
('@s7/1 abc/1', 'GCG', '+', 'PPP'),
('@s8/1 abc/1', 'CGC', '+', 'PPP'),
('@s9/1 abc/1', 'CGT', '+', 'PPP'),
('@s10/1 abc/1', 'TGC', '+', 'PPP'),
('@s11/1 abc/1', 'TCA', '+', 'PPP')]
self.bpsi = BarcodePairedSequenceFastqIterator(self.barcodes,
self.forward,
self.reverse)
barcode_map = pd.Series(
['AAAA', 'AACC', 'TTAA', 'GGAA', 'CGGC'],
name='bc',
index=pd.Index(
['sample1', 'sample2', 'sample3', 'sample4', 'sample5'],
name='id'))
self.barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
def test_barcode_trimming(self):
# these barcodes are longer then the ones in the mapping file, so
# only the first barcode_length bases should be read
barcodes = [('@s1/2 abc/2', 'AAAAG', '+', 'YYYY'),
('@s2/2 abc/2', 'TTAAG', '+', 'PPPP'),
('@s3/2 abc/2', 'AACCG', '+', 'PPPP'),
('@s4/2 abc/2', 'TTAAG', '+', 'PPPP'),
('@s5/2 abc/2', 'AACCG', '+', 'PPPP'),
('@s6/2 abc/2', 'AAAAG', '+', 'PPPP'),
('@s7/2 abc/2', 'CGGCG', '+', 'PPPP'),
('@s8/2 abc/2', 'GGAAG', '+', 'PPPP'),
('@s9/2 abc/2', 'CGGCG', '+', 'PPPP'),
('@s10/2 abc/2', 'CGGCG', '+', 'PPPP'),
('@s11/2 abc/2', 'GGAAG', '+', 'PPPP')]
bpsi = BarcodePairedSequenceFastqIterator(barcodes, self.forward,
self.reverse)
self.check_valid(bpsi, self.barcode_map)
def test_inconsistent_sequence_length_paired(self):
forward = [('@s1/1 abc/1', 'G', '+', 'Y'),
('@s2/1 abc/1', 'CCC', '+', 'PPP'),
('@s3/1 abc/1', 'AAAAA', '+', 'PPPPP'),
('@s4/1 abc/1', 'TTTTTTT', '+', 'PPPPPPP')]
reverse = [('@s1/1 abc/1', 'AAAAAAA', '+', 'YYYYYYY'),
('@s2/1 abc/1', 'TTTTT', '+', 'PPPPP'),
('@s3/1 abc/1', 'GGG', '+', 'PPP'),
('@s4/1 abc/1', 'C', '+', 'P')]
bpsi = BarcodePairedSequenceFastqIterator(self.barcodes, forward,
reverse)
barcode_map = pd.Series(['AAAA', 'AACC'],
name='bc',
index=pd.Index(['sample1', 'sample2'],
name='id'))
barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
demux_data = emp_paired(bpsi, barcode_map)
lengths = [1, 3, 5, 7]
for n in range(1, 6):
with tempfile.TemporaryDirectory() as output_dir:
lengths_ = lengths[0:5 - n] if n < 4 else [1]
# TODO: Remove _PlotQualView wrapper
summarize(output_dir,
_PlotQualView(demux_data, paired=True),
n=n)
plot_fp = os.path.join(output_dir, 'data.jsonp')
with open(plot_fp, 'r') as fh:
jsonp = fh.read()
json_ = jsonp.replace('app.init(', '[').replace(');', ']')
payload = json.loads(json_)[0]
self.assertEqual(payload["totalSeqCount"], 4)
self.assertIn(payload["minSeqLen"]["forward"], lengths_)
self.assertIn(payload["minSeqLen"]["reverse"], lengths_)
self.assertEqual(payload["n"], min(n, 4))