Source: q2-demux
Version: 2019.10.0-1
Control: block 950430 by -1
With pandas 1.0 from experimental:
=================================== FAILURES
===================================
__________________________ SummarizeTests.test_basic
___________________________
self = <q2_demux.tests.test_demux.SummarizeTests testMethod=test_basic>
def test_basic(self):
bsi = BarcodeSequenceFastqIterator(self.barcodes, self.sequences)
barcode_map = pd.Series(
['AAAA', 'AACC'], name='bc',
index=pd.Index(['sample_1', 'sample2'], name='id')
)
barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
demux_data, ecc = emp_single(bsi, barcode_map,
golay_error_correction=False)
# test that an index.html file is created and that it has size > 0
with tempfile.TemporaryDirectory() as output_dir:
# TODO: Remove _PlotQualView wrapper
result = summarize(output_dir, _PlotQualView(demux_data,
> paired=False),
n=2)
q2_demux/tests/test_demux.py:860:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
___________ SummarizeTests.test_inconsistent_sequence_length_paired
____________
self = <q2_demux.tests.test_demux.SummarizeTests
testMethod=test_inconsistent_sequence_length_paired>
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, ecc = emp_paired(bpsi, barcode_map,
golay_error_correction=False)
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)
q2_demux/tests/test_demux.py:1101:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
___________ SummarizeTests.test_inconsistent_sequence_length_single
____________
self = <q2_demux.tests.test_demux.SummarizeTests
testMethod=test_inconsistent_sequence_length_single>
def test_inconsistent_sequence_length_single(self):
sequences = [('@s1/1 abc/1', 'GGGGGGG', '+', 'YYYYYYY'),
('@s2/1 abc/1', 'CCCCC', '+', 'PPPPP'),
('@s3/1 abc/1', 'AAA', '+', 'PPP'),
('@s4/1 abc/1', 'T', '+', 'P')]
bsi = BarcodeSequenceFastqIterator(self.barcodes, sequences)
barcode_map = pd.Series(
['AAAA', 'AACC'], name='bc',
index=pd.Index(['sample1', 'sample2'], name='id')
)
barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
demux_data, ecc = emp_single(bsi, barcode_map,
golay_error_correction=False)
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=False), n=n)
q2_demux/tests/test_demux.py:1063:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
________________________ SummarizeTests.test_paired_end
________________________
self = <q2_demux.tests.test_demux.SummarizeTests testMethod=test_paired_end>
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, ecc = emp_paired(bpsi, barcode_map,
golay_error_correction=False)
with tempfile.TemporaryDirectory() as output_dir:
result = summarize(output_dir, _PlotQualView(demux_data,
> paired=True), n=2)
q2_demux/tests/test_demux.py:978:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
_________________ SummarizeTests.test_phred_score_out_of_range
_________________
self = <q2_demux.tests.test_demux.SummarizeTests
testMethod=test_phred_score_out_of_range>
def test_phred_score_out_of_range(self):
barcodes = self.barcodes[:3]
sequences = [('@s1/1 abc/1', 'GGG', '+', 'jjj'),
('@s2/1 abc/1', 'CCC', '+', 'iii'),
('@s3/1 abc/1', 'AAA', '+', 'hhh')]
bsi = BarcodeSequenceFastqIterator(barcodes, sequences)
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, ecc = emp_single(bsi, barcode_map,
golay_error_correction=False)
with tempfile.TemporaryDirectory() as output_dir:
result = summarize(output_dir, _PlotQualView(demux_data,
> paired=False),
n=50)
q2_demux/tests/test_demux.py:1035:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
__________ SummarizeTests.test_sequence_length_uses_subsample_paired
___________
self = <q2_demux.tests.test_demux.SummarizeTests
testMethod=test_sequence_length_uses_subsample_paired>
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, ecc = emp_paired(bpsi, barcode_map,
golay_error_correction=False)
with tempfile.TemporaryDirectory() as output_dir:
> summarize(output_dir, _PlotQualView(demux_data,
paired=True), n=2)
q2_demux/tests/test_demux.py:1164:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
__________ SummarizeTests.test_sequence_length_uses_subsample_single
___________
self = <q2_demux.tests.test_demux.SummarizeTests
testMethod=test_sequence_length_uses_subsample_single>
def test_sequence_length_uses_subsample_single(self):
random.seed(6) # Will select s1 and s2 which aren't the
shortest ones
sequences = [('@s1/1 abc/1', 'GGGGGGG', '+', 'YYYYYYY'),
('@s2/1 abc/1', 'CCCCC', '+', 'PPPPP'),
('@s3/1 abc/1', 'AAA', '+', 'PPP'),
('@s4/1 abc/1', 'T', '+', 'P')]
bsi = BarcodeSequenceFastqIterator(self.barcodes, sequences)
barcode_map = pd.Series(
['AAAA', 'AACC'], name='bc',
index=pd.Index(['sample1', 'sample2'], name='id')
)
barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
demux_data, ecc = emp_single(bsi, barcode_map,
golay_error_correction=False)
with tempfile.TemporaryDirectory() as output_dir:
> summarize(output_dir, _PlotQualView(demux_data,
paired=False), n=2)
q2_demux/tests/test_demux.py:1131:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
______________________ SummarizeTests.test_single_sample
_______________________
self = <q2_demux.tests.test_demux.SummarizeTests
testMethod=test_single_sample>
def test_single_sample(self):
bsi = BarcodeSequenceFastqIterator(self.barcodes[:1],
self.sequences[:1])
barcode_map = pd.Series(
['AAAA'], name='bc',
index=pd.Index(['sample1'], name='id')
)
barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
demux_data, ecc = emp_single(bsi, barcode_map,
golay_error_correction=False)
# test that an index.html file is created and that it has size > 0
with tempfile.TemporaryDirectory() as output_dir:
# TODO: Remove _PlotQualView wrapper
result = summarize(output_dir, _PlotQualView(demux_data,
> paired=False),
n=1)
q2_demux/tests/test_demux.py:902:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
_______________ SummarizeTests.test_single_sample_multiple_files
_______________
self = <q2_demux.tests.test_demux.SummarizeTests
testMethod=test_single_sample_multiple_files>
def test_single_sample_multiple_files(self):
# Note, this case came up on the QIIME 2 Forum, due to a user
running
# `summarize` with demuxed sequences that all had the same
Sample ID
# in the internal MANIFEST file. With versions of seaborn
greater than
# 0.8.0 this is no longer a problem, but on prior versions, the
user
# would see the following error:
# TypeError: len() of unsized object
files = ['sample1_S0_L001_R1_001.fastq.gz',
'sample2_S0_L001_R1_001.fastq.gz',
'sample3_S0_L001_R1_001.fastq.gz',
'MANIFEST', 'metadata.yml']
for f in files:
shutil.copy(
self.get_data_path('single_sample_multiple_files/%s' % f),
self.temp_dir.name)
demux_data = SingleLanePerSampleSingleEndFastqDirFmt(
self.temp_dir.name, mode='r')
with tempfile.TemporaryDirectory() as output_dir:
# TODO: Remove _PlotQualView wrapper
result = summarize(output_dir, _PlotQualView(demux_data,
> paired=False),
n=1)
q2_demux/tests/test_demux.py:940:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
_____________ SummarizeTests.test_subsample_higher_than_seqs_count
_____________
self = <q2_demux.tests.test_demux.SummarizeTests
testMethod=test_subsample_higher_than_seqs_count>
def test_subsample_higher_than_seqs_count(self):
barcodes = self.barcodes[:1]
sequences = self.sequences[:1]
bsi = BarcodeSequenceFastqIterator(barcodes, sequences)
barcode_map = pd.Series(['AAAA'], name='bc',
index=pd.Index(['sample1'], name='id'))
barcode_map = qiime2.CategoricalMetadataColumn(barcode_map)
demux_data, ecc = emp_single(bsi, barcode_map,
golay_error_correction=False)
with tempfile.TemporaryDirectory() as output_dir:
result = summarize(output_dir, _PlotQualView(demux_data,
> paired=False),
n=50)
q2_demux/tests/test_demux.py:1010:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
q2_demux/_summarize/_visualizer.py:169: in summarize
forward_length_table = _build_seq_len_table(forward_scores)
q2_demux/_summarize/_visualizer.py:109: in _build_seq_len_table
return q2templates.df_to_html(frame)
/usr/lib/python3/dist-packages/q2templates/util.py:45: in df_to_html
with pd.option_context('display.max_colwidth', -1):
/usr/lib/python3/dist-packages/pandas/_config/config.py:407: in __enter__
_set_option(pat, val, silent=True)
/usr/lib/python3/dist-packages/pandas/_config/config.py:127: in _set_option
o.validator(v)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
value = -1
def is_nonnegative_int(value):
"""
Verify that value is None or a positive int.
Parameters
----------
value : None or int
The `value` to be checked.
Raises
------
ValueError
When the value is not None or is a negative integer
"""
if value is None:
return
elif isinstance(value, int):
if value >= 0:
return
msg = "Value must be a nonnegative integer or None"
> raise ValueError(msg)
E ValueError: Value must be a nonnegative integer or None
/usr/lib/python3/dist-packages/pandas/_config/config.py:844: ValueError
