Fpath = filedialog.askdirectory()
# 读取panel表信息
panel_file = Fpath + "/panel.xlsx"
panel_tuple = Fcs.export_panel_tuple(panel_file)
print(panel_tuple)
for filename in [
filename for filename in os.listdir(Fpath)
if os.path.splitext(filename)[1] == ".fcs"
]:
file = Fpath + '/' + filename
fcs = Fcs(file)
pars = fcs.delete_channel(fcs.pars, 89, 115, 140, 115)
# pars = fcs.marker_rename(fcs.pars, *panel_tuple)
# stain_channel_index = fcs.get_stain_channels(pars)
#
# # 添加event_length, 191, 193, 194, 140
# add_channel = ["Event_length", "Ir191Di", "Ir193Di", "Pt194Di", "Ce140Di"]
# add_index = [i + 1 for i in range(0, len(pars)) if pars[i].par_short_name in add_channel]
# stain_channel_index.extend(add_index)
# pars = [pars[i] for i in range(0, len(pars)) if i + 1 in stain_channel_index]
# 根据当前的filename去查找新的name
new_filename = re.sub("-", "", filename)
# new_filename = re.sub("^.+?_", "gsH_", new_filename)
new_file = Fpath + "/WriteFcs/" + new_filename
fcs.write_to(new_file, pars)
if __name__ == '__main__':
###################################################
#### 1.Read FCS file and convert to CSV ####
###################################################
# Choose File Path
Fpath = filedialog.askdirectory()
os.makedirs(Fpath + "/WriteFcs/")
csv_path = Fpath + '/WriteFcs/'
for filename in [
filename for filename in os.listdir(Fpath)
if os.path.splitext(filename)[1] == ".fcs"
]:
file = Fpath + '/' + filename
fcs = Fcs(file)
pars = fcs.pars
new_filename = re.sub("-", "", filename)
new_filename = re.sub("^.+?_", "", new_filename)
# new_filename = re.sub("^.+?_", "", new_filename)
new_file = Fpath + "/WriteFcs/" + new_filename + '.csv'
fcs.write_to(new_file, pars, to='csv')
path = Fpath + "/WriteFcs"
all_df = pd.DataFrame()
for file in os.listdir(path):
df = pd.read_csv(path + '/' + file)
all_df = all_df.append(df)
print("File %s has finished." % file)
all_df.iloc[:, :-1].to_csv(path + '/' + path.split('/')[-2] + '.csv',
index=False)
file = Fpath + '/' + filename
fcs = Fcs(file)
pars = fcs.marker_rename(fcs.pars, *panel_tuple)
stain_channel_index = fcs.get_stain_channels(pars)
# Add event_length, 191, 193, 194, 140
add_channel = ["Event_length", "Ir191Di", "Ir193Di", "Pt194Di", "Ce140Di"]
add_index = [i + 1 for i in range(0, len(pars)) if pars[i].par_short_name in add_channel]
stain_channel_index.extend(add_index)
pars = [pars[i] for i in range(0, len(pars)) if i + 1 in stain_channel_index]
# Rename new file
new_filename = re.sub("-", "", filename)
new_filename = re.sub("^.+?_", "", new_filename)
# new_filename = re.sub("^.+?_", "", new_filename)
new_file = Fpath + "/WriteFcs/" + new_filename
fcs.write_to(new_file, pars, to="csv")
print('All FCS files have been converted to CSV files.', '\n', '-'*100, '\n')
###################################################
#### 2. Calculation ####
###################################################
file_list = os.listdir(csv_path)
label_frequency_all = pd.DataFrame()
ratio_all = pd.DataFrame()
real_all = pd.DataFrame()
real_adjust_all = pd.DataFrame()
confidence_all = pd.DataFrame()
immune_age_all = pd.DataFrame()
ratio34_all = pd.DataFrame()
impair_all = pd.DataFrame()