Test module: gff_gtf_tools.py

tests.gff_gtf_tools.py

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

module_version:1.0 created_on:2013-11-27

gff and gtf tool tests

class tests.gff_gtf_tools.TestGFFGTFTools(methodName='runTest')

Test the class and functions defined in gff_gtf_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 gff and gtf files with different parameters are created in this directory to test the routines with.

test_annotation()

tests for the annotations class

Test object	Expectation
small complex gff file	correct annotation object
set_feature arg not string	TypeError
set_feature arg not in feature	ValueError
types
set_feature correct args	sorting index for just that feature

test_parse_gff_v3()

Test the parsing routine for v3 gff files

Test object	Expectation
simple gff file	correct wigData object with correct wigTrack objects
gff w. incorrect data	IndexError