def create_test_array(): d = {'9':'5', '10':'288', '11':'002556688', '12':'00012355555', '13':'0000013555688', '14':'00002555558', '15':'0000000000355555555557', '16':'000045', '17':'000055', '18':'0005', '19':'00005', '21':'5'} ext_array = IntsStats() for key, values in d.items(): for num in values: ext_array.append(int(key+num)) return ext_array
def _get_lengths_quals_from_file(seq_fpath): 'Given a sequence file it returns the lengths and quals' lengths = IntsStats(init_len=1000) quals = IntsStats(init_len=100) for seq in seqs_in_file(open(seq_fpath)): lengths.append(len(seq)) qual = seq.qual if qual: quals.extend(qual) return lengths, quals
def test_array(): 'Create an extensible array' ext_array = IntsStats(init_len=5) ext_array.append(6) ext_array.append(2) assert ext_array.min == 2 assert ext_array.max == 6 ext_array.append(200) assert ext_array.max == 200 input_ = (3, 5, 7, 7, 38) ext_array = IntsStats(input_) assert ext_array.median == 7
def test_stats_functs(self): 'It test the statistical functions of the class' ext_array = IntsStats() ext_array.append(3) ext_array.append(5) ext_array.append(7) ext_array.append(7) ext_array.append(38) assert ext_array.median == 7 ext_array = IntsStats() ext_array.append(3) ext_array.append(5) ext_array.append(7) ext_array.append(7) assert ext_array.median == 6 ext_array = self.create_test_array() assert ext_array.median == 145 assert round(ext_array.average, 2) == 145.15 assert ext_array.sum == 13354 assert ext_array.count == 92 assert round(ext_array.variance, 2) == 557.43