def read_line(self, line):
info = self._csv.read_line(line)
try:
info[0] = amdis.correct_code(info[0])
except:
return None
try:
info[1] = float(info[1])
except ValueError:
info[1] = None
return None
try:
info[2] = float(info[2])
except ValueError:
print('ERROR: in {0}, value for lim in code {1} is not a number \
or missing.'.format(self._path, info[0]))
sys.exit(2)
try:
info[3] = [int(i) for i in info[3].split("+")]
except:
print('ERROR: in {0}, value for m/z in code {1} is wrong format.'\
.format(self._path, info[0]))
print('It should be one integer, or more separate with "+".')
sys.exit(2)
self._lib[info[0]] = {}
for i in range(1, len(self._headerlist)):
self._lib[info[0]][self._headerlist[i]] = info[i]
return
def CFdict(path, csv):
import amdis
CFdict = {}
with open(path, 'r') as calfile:
for line in calfile:
info = csv.read_line(line)
CFdict[amdis.correct_code(info[0])] = (float(info[-2]),
float(info[-1]))
return CFdict
def main():
options = get_info()
project_name = options.project_name.lower()
sample = options.sample.lower()
code = amdis.correct_code(options.code)
info = init.Info('pyquan.ini')
path = init.Path(project_name, info)
removecode = RemoveCode(path, info, code)
if sample == 'all':
removecode.remove_all()
else:
removecode.remove_code(sample)
print('\a')
return
def scan_amdis(info_old, amdis_dict, csv):
from operator import itemgetter
for i in range(len(info_old)):
info_old[i] = csv.read_line(info_old[i])
try:
info_old[i][1] = float(info_old[i][1])
except:
pass
info_old[i][0] = amdis.correct_code(info_old[i][0])
compound = amdis_dict.pop(info_old[i][0], None)
if compound:
info_old[i][4] = compound
else:
print('{0} not in AMDIS library'.format(info_old[i][0]))
return info_old, amdis_dict
def update_library(amdis_path, lib_path, info, path):
amdis_dict = amdis.read_compounds(amdis_path)
info_old = None
mz_dict = amdis.read_intensity(amdis_path, info)
#open library if exists, and check compound name
if os.path.exists(lib_path):
with open(lib_path, 'r') as lib_old:
lib_old.readline()
info_old = lib_old.readlines()
info_old, amdis_dict = scan_amdis(info_old, amdis_dict, info.csv)
with open(lib_path, 'w') as lib_new:
lib_new.write(
info.csv.make_line(
['Code', 'RT', 'Limit', 'm/z', 'Name', 'Source']))
if info_old:
for line in info_old:
try:
spectrum = mz_dict[line[0]]
m_list = [int(i) for i in line[3].split("+")]
if not all(m in spectrum
for m in [int(i) for i in m_list]):
print('m/z {0} not in mass spectrum of {1},' \
.format(line[3],line[0]),)
line[3] = max(spectrum.items(), \
key=operator.itemgetter(1))[0]
print('m/z changed to {0}'.format(line[3]))
except KeyError:
pass
lib_new.write(info.csv.make_line(line))
if amdis_dict:
for code in amdis_dict:
mass = max(mz_dict[code].items(),
key=operator.itemgetter(1))[0]
lib_new.write(
info.csv.make_line([
amdis.correct_code(code), "", "", mass, "",
amdis_dict[code], ""
]))
return
def ID(self, line):
info = self._csv.read_line(line)
ID = {}
for i in range(1,len(self._itemlist)):
if 'None' in info[i]:
info[i] = ''
elif self._stylelist[i] == 'float':
info[i] = float(info[i])
elif self._stylelist[i] == 'int':
info[i] = int(info[i])
elif self._stylelist[i] == 'list_float':
infolist = []
for item in info[i].split(' '):
if item:
infolist.append(float(item))
info[i] = infolist
elif self._stylelist[i] == 'list_int':
infolist = []
for i in info[i].split(' '):
infolist.append(int(i))
info[i] = infolist
ID[self._itemlist[i]] = info[i]
return amdis.correct_code(info[0]), ID
def code(self, line):
return amdis.correct_code(self._csv.read_line(line)[0])