def get_gene_data(gene_name):
'''
extract expressed tissues list given by the gene name
:param gene_name:
:return:
'''
argvs = get_cli_args()
temp_host_name = argvs.HOST
temp_gene_name = argvs.GENE
if temp_host_name is None:
host_name = "Homo_sapiens"
gene_name = "TGM1"
else:
host_name = modify_host_name(temp_host_name)
gene_name = temp_gene_name
file = "/".join((config.get_unigene_directory(), \
host_name, gene_name + "." + config.get_uigene_extension()))
if my_io.is_valid_gene_file_name(file):
# using f-strings
message = f"\nFound Gene {gene_name} for {host_name}"
else:
print(f"Not found\n\
Gene {gene_name} does not exist for {host_name}. exiting now...")
sys.exit()
fh_in = my_io.get_fh(file, "r")
for line in fh_in:
match = re.search(r'^EXPRESS\s+(\D+)', line)
if match:
tissue_string = match.group(1)
temp_tissue_list = list(tissue_string.split(sep='|'))
tissue_list = sorted([tissue.strip() for tissue in temp_tissue_list])
return message, tissue_list
def get_gene_data(gene_file):
"""
Get Epressed gene names from host file.
:param gene_file: Absolute path to gene file of host
:return: Sorted list of expresssed genes in host
"""
fh_in = my_io.get_fh(gene_file, "r")
tissue_strig = []
for line in fh_in:
if re.search("EXPRESS", line):
line = line.replace("\n", "")
line = re.sub('[A-Z]', "", line)
tissue_strig = line.split("|")
tissue_strig = [x.strip(' ') for x in tissue_strig]
my_io.get_fh(fh_in, "close")
return sorted(tissue_strig)
def test_get_fh_4_OSError():
_create_test_file(FILE_2_TEST)
with pytest.raises(OSError):
my_io.get_fh("does_not_exist.txt", "r")
os.remove(FILE_2_TEST)
def test_get_fh_4_TypeError():
_create_test_file(FILE_2_TEST)
with pytest.raises(TypeError):
my_io.get_fh([], "r")
os.remove(FILE_2_TEST)
def test_get_fh_4_ValueError():
_create_test_file(FILE_2_TEST)
with pytest.raises(ValueError):
my_io.get_fh("test.txt", "rrr")
os.remove(FILE_2_TEST)
def test_existing_get_fh_4_writing():
test = my_io.get_fh(FILE_2_TEST, "w")
assert hasattr(test, "write") == True, "Not able to open for writing"
test.close()
os.remove(FILE_2_TEST)
def test_existing_get_fh_4_reading():
_create_test_file(FILE_2_TEST)
test = my_io.get_fh(FILE_2_TEST, "r")
assert hasattr(test, "readline") == True, "Not able to open for reading"
test.close()
os.remove(FILE_2_TEST)