def test_samtools_index_cmd(): """samtools_index instantiates, runs and returns correct form of cmd-line""" obj = samtools_index.Samtools_Index("samtools") target = ' '.join(["samtools", "index", BAM_FILE]) stats = obj.run(BAM_FILE) assert_equal(stats.command, target)
def test_samtools_index_exec(): """Run samtools_index on test data and compare output to precomputed target""" obj = samtools_index.Samtools_Index("samtools") result = obj.run(BAM_FILE) # test to see if it has produced the bai file. if not os.path.isfile(result.bai): return False
def test_samtools_index_notexec(): """Error thrown if samtools_index exe not executable""" try: obj = samtools_index.Samtools_Index("LICENSE") except NotExecutableError: return True else: return False
def test_samtools_index_exec_notexist(): """Error thrown if samtools_index executable does not exist""" try: obj = samtools_index.Samtools_Index(os.path.join(".", "samtools")) except NotExecutableError: return True else: return False
def test_samtools_index(): """Samtools_index instantiates with cmd-line if Samtools_index is in $PATH""" samtools_index.Samtools_Index("samtools")