def test_source_file_is_stored(self):
peaks1 = PeakSet('ChIP_peaks-ex1.txt')
peaks2 = PeakSet('ChIP_peaks-ex2.txt')
self.assertEqual(peaks1.source_file, 'ChIP_peaks-ex1.txt')
for peak in peaks1:
self.assertEqual(peak.source_file, 'ChIP_peaks-ex1.txt')
self.assertEqual(peaks2.source_file, 'ChIP_peaks-ex2.txt')
for peak in peaks2:
self.assertEqual(peak.source_file, 'ChIP_peaks-ex2.txt')
def test_get_slice(self):
peaks = PeakSet('ChIP_peaks-ex1.txt')
peaks_slice = peaks[1:3]
self.assertTrue(isinstance(peaks_slice, PeakSet))
self.assertEqual(len(peaks_slice), 2)
self.assertEqual(peaks[1], peaks_slice[0])
self.assertEqual(peaks[2], peaks_slice[1])
def test_handling_quoted_chr(self):
peaks = PeakSet('ChIP_peaks-ex5.txt')
self.assertEqual(len(peaks), 5,
"Wrong number of lines read from ChIP-seq file")
peaks_chr = peaks.filterByChr("chr4")
self.assertEqual(len(peaks_chr), 2,
"Wrong number of ChIP-seq records filtered")
def test_write_peaks_summary(self):
# Set up some test data
feature = Feature('CG31973','chr2L','25402','59243','-')
peaks = PeakSet(
peaks_list=(
Peak('chr2L','66711','66911'),
Peak('chr2L','249077','249277'),
Peak('chr2L','605850','606050')))
# Temp output files
fp,summary= tempfile.mkstemp()
# Write peaks to file
ap = AnalysisReportWriter(output.MULTI_LINE,
fields=('feature.id',
'order',
'peak.chr',
'peak.start',
'peak.end',
'dist_closest',
'dist_TSS'),
summary=summary)
ap.write_nearest_peaks(feature,peaks)
ap.close()
# Expected and actual output
expected_output = \
"#feature.id\torder\tpeak.chr\tpeak.start\tpeak.end\tdist_closest\tdist_TSS\n" \
"CG31973\t1 of 3\tchr2L\t66711\t66911\t7468\t7468\n"
actual_output = open(summary,'r').read()
# Check that output matches
self.assertEqual(expected_output,actual_output)
def test_populate_from_list_of_peaks(self):
peaks = PeakSet(peaks_list=(Peak('chr2L', 66711, 66911),
Peak('chr2L', 605850, 606050),
Peak('chr3L', 2258089, 2258289)))
self.assertEqual(peaks.source_file, None)
self.assertEqual(peaks[0], Peak('chr2L', 66711, 66911))
self.assertEqual(peaks[1], Peak('chr2L', 605850, 606050))
self.assertEqual(peaks[2], Peak('chr3L', 2258089, 2258289))
def test_filter_on_peak_position(self):
peaks = PeakSet('ChIP_peaks-ex1.txt')
lower, upper = 12000000, 15000000
peaks_pos = peaks.filterByPosition(upper, lower)
self.assertEqual(len(peaks_pos), 2, "Wrong number of peaks filtered")
for peak in peaks_pos:
print(str(peak))
self.assertTrue((peak.start >= lower and peak.start <= upper),
"Peak should have been filtered out")
def test_reading_in_ChIPseq_data_custom_columns(self):
peaks = PeakSet('ChIP_peaks_multi_columns-ex1.txt', columns=(2, 4, 5))
self.assertEqual(peaks.source_file, 'ChIP_peaks_multi_columns-ex1.txt')
self.assertEqual(len(peaks), 5,
"Wrong number of lines read from ChIP-seq file")
self.assertEqual(peaks[0], Peak('chr3L', 4252919, 4252920))
self.assertEqual(peaks[1], Peak('chr3L', 9502640, 9502641))
self.assertEqual(peaks[2], Peak('chr3L', 12139192, 12139193))
self.assertEqual(peaks[3], Peak('chr3L', 14983597, 14983598))
self.assertEqual(peaks[4], Peak('chr3L', 17004143, 17004144))
def test__eq__(self):
# Test equality of PeakSets
peak_set1 = PeakSet()
peak_set2 = PeakSet()
# Empty feature sets
self.assertEqual(peak_set1, peak_set2)
# Populate
peak_set1.addPeak(Peak('chr2L', '66811', '66812'))
peak_set2.addPeak(Peak('chr2L', '66811', '66812'))
self.assertEqual(peak_set1, peak_set2)
# Add second
peak_set1.addPeak(Peak('chr2L', '249177', '605951'))
self.assertNotEqual(peak_set1, peak_set2)
peak_set2.addPeak(Peak('chr2L', '249177', '605951'))
self.assertEqual(peak_set1, peak_set2)
# Add third
peak_set1.addPeak(Peak('chr2L', '605650', '605850'))
peak_set2.addPeak(Peak('chr2L', '605850', '606050'))
self.assertNotEqual(peak_set1, peak_set2)
def test_filter_on_chromosome(self):
peaks_chr = PeakSet('ChIP_peaks-ex2.txt')
chromosome = 'chr2L'
self.assertEqual(len(peaks_chr), 10,
"Wrong number of lines from ChIP-seq file")
peaks_chr = peaks_chr.filterByChr(chromosome)
self.assertEqual(
len(peaks_chr), 5,
"Wrong number of lines from ChIP-seq after chr filter")
for peak in peaks_chr:
self.assertTrue((peak.chrom == chromosome),
"Wrong chromosome name filtered by chr")
def test_ChIP_peak_inside_region(self):
peaks = PeakSet('ChIP_peaks-ex1.txt')
lower, upper = 4252000, 4254000
self.assertTrue(peaks[0].insideRegion(upper, lower),
"ChIP peak should be in region")
self.assertTrue(peaks[0].insideRegion(lower, upper),
"ChIP peak should be in region (reversed limits)")
upper, lower = 4252000, 4242000
self.assertFalse(peaks[0].insideRegion(upper, lower),
"ChIP peak should not be inside region")
self.assertFalse(
peaks[0].insideRegion(lower, upper),
"ChIP peak should not be inside region (reversed limits")
def test_closest_transcript_to_peak(self):
features = FeatureSet('Transcripts-ex1.txt')
feature1 = features[1]
feature2 = features[2]
peaks = PeakSet('ChIP_peaks-ex1.txt')
peak = peaks[0]
nearest = GetNearestTranscriptToPeak(feature1, feature2, peak)
# 2nd feature should be closer than first
self.assertEqual(nearest, feature1,
"Wrong transcript selected as nearest")
# test when only one is set
nearest = GetNearestTranscriptToPeak(None, feature2, peak)
self.assertEqual(nearest, feature2,
"Wrong transcript selected as nearest")
def test_sort_by_distance_from(self):
peaks_sort = PeakSet('ChIP_peaks-ex1.txt')
position = 12000000
# Do the sorting
peaks_sort.sortByDistanceFrom(position)
# Check that each distance is greater than the previous one
last_peak = None
for peak in peaks_sort:
if not last_peak:
last_peak = peak
else:
self.assertTrue((abs(peak.start - position) >=
abs(last_peak.start - position)),
"Sort by distance failed")
def test_reading_in_ChIPseq_with_id_column(self):
peaks = PeakSet('ChIP_peaks_multi_columns-ex1.txt',
columns=(2, 4, 5),
id_column=1)
self.assertEqual(peaks.source_file, 'ChIP_peaks_multi_columns-ex1.txt')
self.assertEqual(len(peaks), 5,
"Wrong number of lines read from ChIP-seq file")
self.assertEqual(peaks[0], Peak('chr3L', 4252919, 4252920, id="peak1"))
self.assertEqual(peaks[1], Peak('chr3L', 9502640, 9502641, id="peak2"))
self.assertEqual(peaks[2], Peak('chr3L',
12139192,
12139193,
id="peak3"))
self.assertEqual(peaks[3], Peak('chr3L',
14983597,
14983598,
id="peak4"))
self.assertEqual(peaks[4], Peak('chr3L',
17004143,
17004144,
id="peak5"))
def setUp(self):
# Set up some test data
self.feature = Feature('CG31973','chr2L','25402','59243','-')
self.peaks = PeakSet(
peaks_list=(
Peak('chr2L','66711','66911'),
Peak('chr2L','249077','249277'),
Peak('chr2L','605850','606050')))
self.single_line_fields = ('feature.id',
'number_of_results',
'list(peak.chr,peak.start,peak.end,'
'dist_closest,dist_TSS)')
self.single_line_fields_extra_data = ('feature.id',
'cutoff',
'number_of_results',
'list(peak.chr,peak.start,peak.end,'
'dist_closest,dist_TSS)')
self.multi_line_fields = ('feature.id',
'order',
'peak.chr',
'peak.start',
'peak.end',
'dist_closest',
'dist_TSS')
def test_get_item(self):
peaks = PeakSet('ChIP_peaks-ex1.txt')
peak = peaks[2]
self.assertEqual(peak, Peak('chr3L', '12139192', '12139193'))
def test_is_summit_data(self):
peaks = PeakSet('ChIP_peaks-ex1.txt')
self.assertTrue(peaks.isSummit(), "ChIP data are summits")
peaks = PeakSet('ChIP_peaks-ex5.txt')
self.assertFalse(peaks.isSummit(), "ChIP data are not summits")
