def generate_isotope_patterns(config,verbose=True):
from pySpatialMetabolomics.parse_databases import parse_databases
import pickle
# Extract variables from config dict
db_filename = config['file_inputs']['database_file']
db_dump_folder = config['file_inputs']['database_load_folder']
isocalc_sig = float(config['isotope_generation']['isocalc_sig'])
isocalc_resolution = float(config['isotope_generation']['isocalc_resolution'])
if len(config['isotope_generation']['charge']) > 1:
print 'Warning: only first charge state currently accepted'
charge = int('{}{}'.format(config['isotope_generation']['charge'][0]['polarity'],
config['isotope_generation']['charge'][0][
'n_charges'])) # currently only supports first charge!!
adducts = [a['adduct'] for a in config['isotope_generation']['adducts']]
# Read in molecules
sum_formulae = parse_databases.read_generic_csv(db_filename)
if '' in sum_formulae:
if verbose:
print 'empty sf removed from list'
del sum_formulae['']
# Check if already genrated and load if possible, otherwise calculate fresh
db_name = os.path.splitext(os.path.basename(db_filename))[0]
mz_list = {}
for adduct in adducts:
load_file = '{}/{}_{}_{}_{}.dbasedump'.format(db_dump_folder, db_name, adduct, isocalc_sig, isocalc_resolution)
if os.path.isfile(load_file):
if verbose:
print "{} -> loading".format(load_file)
mz_list_tmp = pickle.load(open(load_file, 'r'))
else:
if verbose:
print "{} -> generating".format(load_file)
mz_list_tmp = calculate_isotope_patterns(sum_formulae, adduct=adduct, isocalc_sig=isocalc_sig,
isocalc_resolution=isocalc_resolution, charge=charge)
if db_dump_folder != "":
pickle.dump(mz_list_tmp, open(load_file, 'w'))
# add patterns to total list
for sum_formula in sum_formulae:
if sum_formula not in mz_list_tmp:# could be missing if [M-a] would have negative atoms
continue
if sum_formula not in mz_list:
mz_list[sum_formula]={}
## this limit of 4 is hardcoded to reduce the number of calculations
n = np.min([4,len(mz_list_tmp[sum_formula][adduct][0])])
mz_list[sum_formula][adduct] = [mz_list_tmp[sum_formula][adduct][0][0:n],mz_list_tmp[sum_formula][adduct][1][0:n]]
if verbose:
print 'all isotope patterns generated and loaded'
return sum_formulae, adducts, mz_list
def generate_isotope_patterns(config):
from pySpatialMetabolomics.parse_databases import parse_databases
import pickle
### We simulate a mass spectrum for each sum formula/adduct combination. This generates a set of isotope patterns (see http://www.mi.fu-berlin.de/wiki/pub/ABI/QuantProtP4/isotope-distribution.pdf) which can provide additional informaiton on the molecule detected. This gives us a list of m/z centres for the molecule
def calcualte_isotope_patterns(sum_formulae,adducts='',isocalc_sig=0.01,isocalc_resolution = 200000.,isocalc_do_centroid = True, charge='1'):
### Generate a mz list of peak centroids for each sum formula with the given adduct
# todo - parse sum formula and adduct properly so that subtractions (losses) can be utilised (this code already exists somewhere)
mz_list={}
for n,sum_formula in enumerate(sum_formulae):
isotope_ms = pyisocalc.isodist(sum_formula+adduct,plot=False,sigma=isocalc_sig,charges=charge,resolution=isocalc_resolution,do_centroid=isocalc_do_centroid)
if not sum_formula in mz_list:
mz_list[sum_formula] = {}
mz_list[sum_formula][adduct] = isotope_ms.get_spectrum(source='centroids')
return mz_list
# Extract variables from config dict
db_filename = config['file_inputs']['database_file']
db_dump_folder = config['file_inputs']['database_load_folder']
isocalc_sig = config['isotope_generation']['isocalc_sig']
isocalc_resolution = config['isotope_generation']['isocalc_resolution']
if len(config['isotope_generation']['charge']) > 1:
print 'Warning: only first charge state currently accepted'
charge = int('{}{}'.format(config['isotope_generation']['charge'][0]['polarity'], config['isotope_generation']['charge'][0]['n_charges'])) #currently only supports first charge!!
adducts=[a['adduct'] for a in config['isotope_generation']['adducts']]
# Read in molecules
sum_formulae = parse_databases.read_generic_csv(db_filename)
# Check if already genrated and load if possible, otherwise calculate fresh
db_name = os.path.splitext(os.path.basename(db_filename))[0]
mz_list={}
for adduct in adducts:
load_file = '{}/{}_{}_{}_{}.dbasedump'.format(db_dump_folder,db_name,adduct,isocalc_sig,isocalc_resolution)
if os.path.isfile(load_file):
mz_list_tmp = pickle.load(open(load_file,'r'))
else:
mz_list_tmp = calcualte_isotope_patterns(sum_formulae,adducts=(adduct,),isocalc_sig=isocalc_sig,isocalc_resolution=isocalc_resolution,charge=charge)
if db_dump_folder != "":
pickle.dump(mz_list_tmp,open(load_file,'w'))
# add patterns to total list
for sum_formula in mz_list_tmp:
if not sum_formula in mz_list:
mz_list[sum_formula] = {}
mz_list[sum_formula][adduct] = mz_list_tmp[sum_formula][adduct]
print 'all isotope patterns generated and loaded'
return sum_formulae,adducts,mz_list
def generate_isotope_patterns(config, verbose=True):
from pySpatialMetabolomics.parse_databases import parse_databases
import pickle
# Extract variables from config dict
db_filename = config['file_inputs']['database_file']
db_dump_folder = config['file_inputs']['database_load_folder']
isocalc_sig = float(config['isotope_generation']['isocalc_sig'])
isocalc_resolution = float(
config['isotope_generation']['isocalc_resolution'])
if len(config['isotope_generation']['charge']) > 1:
print 'Warning: only first charge state currently accepted'
charge = int('{}{}'.format(
config['isotope_generation']['charge'][0]['polarity'],
config['isotope_generation']['charge'][0]
['n_charges'])) # currently only supports first charge!!
adducts = [a['adduct'] for a in config['isotope_generation']['adducts']]
# Read in molecules
sum_formulae = parse_databases.read_generic_csv(db_filename)
if '' in sum_formulae:
if verbose:
print 'empty sf removed from list'
del sum_formulae['']
# Check if already genrated and load if possible, otherwise calculate fresh
db_name = os.path.splitext(os.path.basename(db_filename))[0]
mz_list = {}
for adduct in adducts:
load_file = '{}/{}_{}_{}_{}.dbasedump'.format(db_dump_folder, db_name,
adduct, isocalc_sig,
isocalc_resolution)
if os.path.isfile(load_file):
if verbose:
print "{} -> loading".format(load_file)
mz_list_tmp = pickle.load(open(load_file, 'r'))
else:
if verbose:
print "{} -> generating".format(load_file)
mz_list_tmp = calculate_isotope_patterns(
sum_formulae,
adduct=adduct,
isocalc_sig=isocalc_sig,
isocalc_resolution=isocalc_resolution,
charge=charge)
if db_dump_folder != "":
pickle.dump(mz_list_tmp, open(load_file, 'w'))
# add patterns to total list
for sum_formula in sum_formulae:
if sum_formula not in mz_list_tmp: # could be missing if [M-a] would have negative atoms
continue
if sum_formula not in mz_list:
mz_list[sum_formula] = {}
## this limit of 4 is hardcoded to reduce the number of calculations
n = np.min([4, len(mz_list_tmp[sum_formula][adduct][0])])
mz_list[sum_formula][adduct] = [
mz_list_tmp[sum_formula][adduct][0][0:n],
mz_list_tmp[sum_formula][adduct][1][0:n]
]
if verbose:
print 'all isotope patterns generated and loaded'
return sum_formulae, adducts, mz_list