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from decimal import Decimal
class peak(object):
def __init__(self, mass, inten, charge):
self.mass = mass
self.inten = inten
self.charge = charge
def to_string(self):
print self.mass, self.inten, self.charge
class spec(object):
def __init__(self):
self.id = 0
self.scan = 0
self.rentention = 0.0
self.activation = ""
self.ms_one_id = 0
self.ms_one_scan = 0
self.pre_mz = Decimal(0.0)
self.pre_charge = 0
self.pre_mass = Decimal(0.0)
self.pre_inten = Decimal(0.0)
self.feature_id = 0
self.feature_inten = Decimal(0.0)
self.peak_lst = []
def add_id(self, id):
self.id = id
def add_scan(self, scan):
self.scan = scan
def add_retention(self, time):
self.rentention = time
def add_act(self, act):
self.activation = act
def add_ms_one_id(self, id):
self.ms_one_id = id
def add_ms_one_scan(self, scan):
self.ms_one_scan = scan
def add_mz(self, mz):
self.pre_mz = mz
def add_charge(self, charge):
self.pre_charge = charge
def add_mass(self, mass):
self.pre_mass = mass
def add_inten(self, inten):
self.pre_inten = inten
def add_feature_id(self, id):
self.feature_id = id
def add_feature_inten(self, inten):
self.feature_inten = inten
def add_peak(self, p):
self.peak_lst.append(p)
def to_file(self, filename):
out = open(filename, "a")
out.write("BEGIN IONS\n")
out.write("ID=" + str(self.id) + "\n")
out.write("SCANS=" + str(self.scan) + "\n")
out.write("RETENTION_TIME=" + str(self.rentention) + "\n")
out.write("ACTIVATION=" + self.activation + "\n")
out.write("MS_ONE_ID=" + str(self.ms_one_id) + "\n")
out.write("MS_ONE_SCAN=" + str(self.ms_one_scan) + "\n")
out.write("PRECURSOR_MZ=" + str(self.pre_mz) + "\n")
out.write("PRECURSOR_CHARGE=" + str(self.pre_charge) + "\n")
out.write("PRECURSOR_MASS=" + str(self.pre_mass) + "\n")
out.write("PRECURSOR_INTENSITY=" + str(self.pre_inten) + "\n")
out.write("FEATURE_ID=" + str(self.feature_id) + "\n")
out.write("FEATURE_INTENSITY=" + str(self.feature_inten) + "\n")
for p in self.peak_lst:
out.write(str(p.mass) + "\t" + str(p.inten) + "\t" + str(p.charge) + "\n")
out.write("END IONS\n\n")
def readMsAlign(filename):
msalign_file = open(filename, 'r').readlines()
idx = 0
spec_lst = []
while (idx < len(msalign_file)):
line = msalign_file[idx].rstrip('\r\n')
if line == "BEGIN IONS" :
sp = spec()
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_id(int(float(line.split("=")[1])))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_scan(int(float(line.split("=")[1])))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_retention(float(line.split("=")[1]))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_act(line.split("=")[1])
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_ms_one_id(int(float(line.split("=")[1])))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_ms_one_scan(int(float(line.split("=")[1])))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_mz(Decimal(line.split("=")[1]))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_charge(int(float(line.split("=")[1])))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_mass(Decimal(line.split("=")[1]))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_inten(Decimal(line.split("=")[1]))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_feature_id(int(float(line.split("=")[1])))
idx = idx + 1
line = msalign_file[idx].rstrip('\r\n')
sp.add_feature_inten(Decimal(line.split("=")[1]))
idx = idx + 1
while (idx < len(msalign_file)):
line = msalign_file[idx].rstrip('\r\n')
if line == "END IONS":
spec_lst.append(sp)
break;
tmp = line.split("\t")
p = peak(Decimal(tmp[0]), Decimal(tmp[1]), tmp[2])
sp.add_peak(p)
idx = idx + 1
idx = idx + 1
return spec_lst;
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