wub.tests package

Submodules

wub.tests.test_bam_compare module

class wub.tests.test_bam_compare.TestBamCompare(methodName='runTest')

Bases: unittest.case.TestCase

Test BAM comparison test.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_bam_read_counter()

Test read_counter wrapper.

wub.tests.test_bam_read_counter module

class wub.tests.test_bam_read_counter.TestBamReadCounter(methodName='runTest')

Bases: unittest.case.TestCase

Test BAM read counter wrapper.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_bam_read_counter()

Test read_counter wrapper.

wub.tests.test_bam_stats module

class wub.tests.test_bam_stats.TestBamStats(methodName='runTest')

Bases: unittest.case.TestCase

Test BAM statistics functions.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_error_and_read_stats()

Test the gathering of error and read statistics.

test_fragment_stats()

Test the gathering of fragment statistics.

test_pileup_stats()

Test the gathering read statistics.

test_read_stats()

Test the gathering read statistics.

wub.tests.test_blastn_coord_parse module

class wub.tests.test_blastn_coord_parse.TestBlastnCoordParse(methodName='runTest')

Bases: unittest.case.TestCase

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_nucmer_coord_parse()

Test blastn outfmt 6 cooridnate parsing.

wub.tests.test_contig_stats module

class wub.tests.test_contig_stats.TestContigStats(methodName='runTest')

Bases: unittest.case.TestCase

Test N50 utility function.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_N50()

Test calculation of N50.

wub.tests.test_example module

class wub.tests.test_example.ExampleTest(methodName='runTest')

Bases: unittest.case.TestCase

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_success()

wub.tests.test_mappers_lastal module

class wub.tests.test_mappers_lastal.TestMappersLastal(methodName='runTest')

Bases: unittest.case.TestCase

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_lastal_compare_genomes(**kwargs)

test_parse_lastal_difference()

test_parse_lastal_identical()

test_parse_lastal_zero()

wub.tests.test_nucmer_coord_parse module

class wub.tests.test_nucmer_coord_parse.TestNucmerCoordParse(methodName='runTest')

Bases: unittest.case.TestCase

Test numcmer cooridnate parsing.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_nucmer_coord_parse()

Test parsing of nucmer coordinate files.

wub.tests.test_simulate_genome module

class wub.tests.test_simulate_genome.TestSimulateGenome(methodName='runTest')

Bases: unittest.case.TestCase

Test genome simulation utilities.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_simulate_fragment()

Test fragment simulator.

test_simulate_fragment_edge()

Test fragment simulator (edge case).

test_simulate_genome()

Test genome simulator.

wub.tests.test_simulate_seq module

class wub.tests.test_simulate_seq.TestSimulateSeq(methodName='runTest')

Bases: unittest.case.TestCase

Test sequence simulation utilities.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_add_errors()

Test function adding sequencing errors.

test_cigar_list_to_string()

Test formatting of cigar strings.

test_compress_raw_cigar_list()

Test compression of raw cigar lists.

test_simulate_sequencing_errors()

Test function simulating sequencing errors.

wub.tests.test_util_parse module

class wub.tests.test_util_parse.TestUtilParse(methodName='runTest')

Bases: unittest.case.TestCase

Test parsing utilities.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_args_string_to_dict()

Test parsing of dictionaries encoded in separated strings.

test_args_string_to_dict_empty()

Test parsing of dictionaries encoded in separated strings (empty input).

test_normalise_array()

Test array normalization.

test_separated_list_to_floats()

Test parsing of separated lists.

wub.tests.test_util_seq module

class wub.tests.test_util_seq.TestUtilSeq(methodName='runTest')

Bases: unittest.case.TestCase

Test sequence utilities.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_alignment_stats()

Test calculation of alignment statistics.

test_mean_qscore()

Test mean q score calculation.

test_mean_qscore_large()

Test mean q score calculation (large identical input).

test_mock_qualities()

Test quality mocking function.

test_new_dna_record()

Test the construction of new DNA SeqRecord.

test_phred_to_prob()

Test error probability to phred score conversion.

test_prob_to_phred()

Test error probability to phred score conversion.

test_prob_to_phred_max()

Test error probability to phred score conversion (very small error).

test_reverse_complement()

Test reverse complementing.

wub.tests.test_wrappers_dnadiff module

class wub.tests.test_wrappers_dnadiff.TestWrappersDnadiff(methodName='runTest')

Bases: unittest.case.TestCase

Test dnadiff wrapper.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_dnadiff(**kwargs)

Test dnadiff wrapper.

Module contents