def test_make_header_single_line_custom_feature_type(self):
ap = AnalysisReporter(output.SINGLE_LINE,
fields=('peak.chr',
'peak.start',
'peak.end',
'number_of_results',
'list(feature.id)'),
feature_type='gene',
max_hits=2)
self.assertEqual(ap.make_header(),
"peak.chr\tpeak.start\tpeak.end\tnumber_of_results\tgene.id_1\tgene.id_2")
def test_make_header_single_line_custom_feature_type(self):
ap = AnalysisReporter(output.SINGLE_LINE,
fields=('peak.chr',
'peak.start',
'peak.end',
'number_of_results',
'list(feature.id)'),
feature_type='gene',
max_hits=2)
self.assertEqual(ap.make_header(),
"peak.chr\tpeak.start\tpeak.end\tnumber_of_results\tgene.id_1\tgene.id_2")
def test_make_header_single_line_arbitrary_field(self):
ap = AnalysisReporter(output.SINGLE_LINE,
fields=('peak.chr',
'peak.start',
'peak.end',
'cutoff',
'number_of_results',
'list(feature.id)'),
max_hits=2)
self.assertEqual(ap.make_header(),
"peak.chr\tpeak.start\tpeak.end\tcutoff\tnumber_of_results\tfeature.id_1\tfeature.id_2")
def test_make_header_multi_line_custom_feature_type(self):
ap = AnalysisReporter(output.MULTI_LINE,
fields=('feature.id',
'feature.chr',
'feature.start',
'feature.end',
'peak.chr',
'peak.start',
'peak.end'),
feature_type='gene',
max_hits=2)
self.assertEqual(ap.make_header(),
"gene.id\tgene.chr\tgene.start\tgene.end\tpeak.chr\tpeak.start\tpeak.end")
def test_make_header_multi_line_custom_feature_type(self):
ap = AnalysisReporter(output.MULTI_LINE,
fields=('feature.id',
'feature.chr',
'feature.start',
'feature.end',
'peak.chr',
'peak.start',
'peak.end'),
feature_type='gene',
max_hits=2)
self.assertEqual(ap.make_header(),
"gene.id\tgene.chr\tgene.start\tgene.end\tpeak.chr\tpeak.start\tpeak.end")
def test_make_header_multi_line_arbitrary_field(self):
ap = AnalysisReporter(output.MULTI_LINE,
fields=('feature.id',
'feature.chr',
'feature.start',
'feature.end',
'cutoff',
'peak.chr',
'peak.start',
'peak.end'),
max_hits=2)
self.assertEqual(ap.make_header(),
"feature.id\tfeature.chr\tfeature.start\tfeature.end\tcutoff\tpeak.chr\tpeak.start\tpeak.end")
def test_report_nearest_features_multi_line_max_hits(self):
# Expected lines
expected = (
"chr2L\t66811\t66812\t1 of 2\tCG31973\t7568\t7568",
"chr2L\t66811\t66812\t2 of 2\tCG2674-RE\t40091\t40091",
)
# Set up to report some stuff
ap = AnalysisReporter(output.MULTI_LINE,
fields=self.multi_line_fields,
max_hits=2)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_features(self.peak,
self.features),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_peaks_multi_line_max_hits(self):
# Expected lines
expected = (
"CG31973\t1 of 2\tchr2L\t66711\t66911\t7468\t7468",
"CG31973\t2 of 2\tchr2L\t249077\t249277\t189834\t189834",
)
# Set up to report some stuff
ap = AnalysisReporter(output.MULTI_LINE,
fields=self.multi_line_fields,
max_hits=2)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_peaks(self.feature,
self.peaks),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_features_multi_line_max_hits(self):
# Expected lines
expected = (
"chr2L\t66811\t66812\t1 of 2\tCG31973\t7568\t7568",
"chr2L\t66811\t66812\t2 of 2\tCG2674-RE\t40091\t40091",
)
# Set up to report some stuff
ap = AnalysisReporter(output.MULTI_LINE,
fields=self.multi_line_fields,
max_hits=2)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_features(self.peak,
self.features),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_peaks_multi_line_max_hits(self):
# Expected lines
expected = (
"CG31973\t1 of 2\tchr2L\t66711\t66911\t7468\t7468",
"CG31973\t2 of 2\tchr2L\t249077\t249277\t189834\t189834",
)
# Set up to report some stuff
ap = AnalysisReporter(output.MULTI_LINE,
fields=self.multi_line_fields,
max_hits=2)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_peaks(self.feature,
self.peaks),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_features_single_line(self):
# Expected lines
expected = (
"chr2L\t66811\t66812\t3\t"
"CG31973\t7568\t7568\t"
"CG2674-RE\t40091\t40091\t"
"CG2674-RC\t41114\t41114",
)
# Set up to report some stuff
ap = AnalysisReporter(output.SINGLE_LINE,
fields=self.single_line_fields)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_features(self.peak,
self.features),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_peaks_single_line(self):
# Expected lines
expected = (
"CG31973\t3\t"
"chr2L\t66711\t66911\t7468\t7468\t"
"chr2L\t249077\t249277\t189834\t189834\t"
"chr2L\t605850\t606050\t546607\t546607",
)
# Set up to report some stuff
ap = AnalysisReporter(output.SINGLE_LINE,
fields=self.single_line_fields)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_peaks(self.feature,
self.peaks),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_features_single_line(self):
# Expected lines
expected = (
"chr2L\t66811\t66812\t3\t"
"CG31973\t7568\t7568\t"
"CG2674-RE\t40091\t40091\t"
"CG2674-RC\t41114\t41114",
)
# Set up to report some stuff
ap = AnalysisReporter(output.SINGLE_LINE,
fields=self.single_line_fields)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_features(self.peak,
self.features),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_peaks_single_line(self):
# Expected lines
expected = (
"CG31973\t3\t"
"chr2L\t66711\t66911\t7468\t7468\t"
"chr2L\t249077\t249277\t189834\t189834\t"
"chr2L\t605850\t606050\t546607\t546607",
)
# Set up to report some stuff
ap = AnalysisReporter(output.SINGLE_LINE,
fields=self.single_line_fields)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_peaks(self.feature,
self.peaks),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_features_single_line_extra_data(self):
# Expected lines
expected = (
"chr2L\t66811\t66812\t100000\t2\t"
"CG31973\t7568\t7568\t"
"CG2674-RE\t40091\t40091",
)
# Set up to report some stuff
ap = AnalysisReporter(output.SINGLE_LINE,
fields=self.single_line_fields_extra_data,
max_hits=2)
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_features(self.peak,
self.features,
cutoff=100000),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_peaks_single_line_extra_data(self):
# Expected lines
expected = (
"CG31973\t100000\t2\t"
"chr2L\t66711\t66911\t7468\t7468\t"
"chr2L\t249077\t249277\t189834\t189834",
)
# Set up to report some stuff
ap = AnalysisReporter(output.SINGLE_LINE,
fields=self.single_line_fields_extra_data,
max_hits=2,
null_placeholder='.')
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_peaks(self.feature,
self.peaks,
cutoff=100000),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_peaks_multi_line_pad(self):
# Expected lines
expected = (
"CG31973\t1 of 3\tchr2L\t66711\t66911\t7468\t7468",
"CG31973\t2 of 3\tchr2L\t249077\t249277\t189834\t189834",
"CG31973\t3 of 3\tchr2L\t605850\t606050\t546607\t546607",
"CG31973\t.\t.\t.\t.\t.\t.",
)
# Set up to report some stuff
ap = AnalysisReporter(output.MULTI_LINE,
fields=self.multi_line_fields,
max_hits=4,
pad=True,
null_placeholder='.')
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_peaks(self.feature,
self.peaks),
expected):
self.assertEqual(line,expected_line)
def test_report_nearest_peaks_multi_line_pad(self):
# Expected lines
expected = (
"CG31973\t1 of 3\tchr2L\t66711\t66911\t7468\t7468",
"CG31973\t2 of 3\tchr2L\t249077\t249277\t189834\t189834",
"CG31973\t3 of 3\tchr2L\t605850\t606050\t546607\t546607",
"CG31973\t.\t.\t.\t.\t.\t.",
)
# Set up to report some stuff
ap = AnalysisReporter(output.MULTI_LINE,
fields=self.multi_line_fields,
max_hits=4,
pad=True,
null_placeholder='.')
# Check that output matches
for line,expected_line in izip_longest(
ap.report_nearest_peaks(self.feature,
self.peaks),
expected):
self.assertEqual(line,expected_line)
def test_make_header_multi_line(self):
ap = AnalysisReporter(output.MULTI_LINE,
fields=('feature.id',
'feature.chr',
'feature.start',
'feature.end',
'peak.chr',
'peak.start',
'peak.end'))
self.assertEqual(ap.make_header(),
"feature.id\tfeature.chr\tfeature.start\tfeature.end\tpeak.chr\tpeak.start\tpeak.end")
ap = AnalysisReporter(output.MULTI_LINE,
fields=('feature.id',
'feature.chr',
'feature.start',
'feature.end',
'peak.chr',
'peak.start',
'peak.end'),
max_hits=2)
self.assertEqual(ap.make_header(),
"feature.id\tfeature.chr\tfeature.start\tfeature.end\tpeak.chr\tpeak.start\tpeak.end")
