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)