def test_05_identify(self):
input_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output","pseudoSE")))
output_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output")))
args = docopt(doc, ["-s","identify","-e","identify","-c",config_file,\
"-i",input_folder,"-o",output_folder])
starpa.main(args)
def test_03_sort(self):
input_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output","align")))
output_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output")))
args = docopt(doc, ["-s","sam_sort","-e","sam_sort","-c",config_file,\
"-i",input_folder,"-o",output_folder])
starpa.main(args)
def test_07_quantify(self):
input_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output","cluster")))
output_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output")))
args = docopt(doc, ["-s","quantify","-e","quantify","-c",config_file,\
"-i",input_folder,"-o",output_folder])
starpa.main(args)
shutil.rmtree(output_folder)
def test_01_trim(self):
if '__pypy__' in sys.builtin_module_names:
return
input_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","fq")))
output_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output")))
args = docopt(doc, ["-s","trim","-e","trim","-c",config_file,\
"-i",input_folder,"-o",output_folder])
starpa.main(args)
def test_13sens_SE_full(self):
if '__pypy__' in sys.builtin_module_names:
#in pypy the cutadapt does not work, prepared input is used
input_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","trim_SE_output")))
start_task = "align"
else:
input_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","fq")))
start_task = "trim"
output_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output_SE_sens")))
args = docopt(doc, ["-s",start_task,"-e","quantify", "-c", config_file_sens_SE,\
"-i",input_folder,"-o",output_folder])
starpa.main(args)
def test_02_align(self):
output_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output")))
if '__pypy__' in sys.builtin_module_names:
#in pypy the cutadapt does not work, prepared input is used
input_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","trim_output")))
else:
input_folder = os.path.normpath(os.path.join(os.path.dirname(os.path.realpath(__file__)),
os.path.join("data","output","trim")))
args = docopt(doc, ["-s","align","-e","align","-c",config_file,\
"-i",input_folder,"-o",output_folder])
starpa.main(args)
