Test module: wig_tools.py

tests.wig_tools.py

A module containing tests for the wig_tools module I’m using in wig_tools.py. These tests use the standard unittest package and extend the unittest.TestCase class.

module_version:1.0 created_on:2013-11-22

wig tool tests

class tests.wig_tools.TestWigTools(methodName='runTest')

Test the class and functions defined in wig_tools.py.

Each function is tested with existing and non-existent instances of the file or path type that it is designed for. We also test that providing non- string basic python objects produces string representations and doesn’t case a failure.

setUp()

Initialize the framework for testing.

Define and create a new system temporary directory with the tempfile package for use as an existing directory. A range of wig files with different parameters are created in this directory to test the routines with.

test_wigData_BigWig()

test that the wigData class correctly reads BigWig files

Test object	Expectation
filename not a String	TypeError
file doesn’t exist	IOError
bigWigToWig binary doesn’t exist	IOError
correct args	correct wigData object

test_wigData_and_wigTrack_set_region()

test region setter raises sensible errors in wigTrack & wigData

Test object	Expectation
whole chromosome selection	correctly set region

test_wigData_multi_chromosome()

test the behaviour of wigData with a file with multiple chromosomes

Test object	Expectation
multi_chr complex wigfile	correct wigData object with correct wigTrack objects

test_wigTrack_fixedStep()

Test the behaviour of wigTrack with fixedStep wig files

test_wigTrack_region_functions()

test that the region related class functions work correctly

Test object	Expectation
no region set	raise ValueError
len chr1:10000-50000	40 kb
npoints chr1:10000-50000	11
data chr1:10000-50000	tuple, 0:positions 1:data
max chr1:10000-50000	3
min chr1:10000-50000	1
mean datapoint	1.4692307692307693
mean basesignal	0.0050043231063484159

test_wigTrack_variableStep()

Test the behaviour of wigTrack with variableStep wig files

Test object	Expectation
simple wigfile	correct wigTrack object
complex wigfile	correct wigTrack object