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_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_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_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")
