add -offset argument to CLI for isolation offset.

RawQuant/RawQuant.py

@@ -23,7 +23,7 @@
 
 class RawQuant:
 
-    def __init__(self, RawFile, order='auto', disable_bar=False):
+    def __init__(self, RawFile, order='auto', disable_bar=False, boxcar=False, isolationOffset=None):
 
         self.disable_bar = disable_bar
 
@@ -141,23 +141,12 @@ def __init__(self, RawFile, order='auto', disable_bar=False):
         if 'Master Scan Number:' in labels:
             self.flags['MasterScanNumber'] = True
 
-        # get the isolation window offset, if there is one
-        # if the system is linux, this seems to fail, so for now we will check that and skip if it is so
-
-        if (sys.platform is 'linux') | (sys.platform is 'darwin'):
-
-            offset = 0.0
-
+        if isolationOffset is not None:
+            self.MetaData['Offset'] = float(isolationOffset)
         else:
+            self.MetaData['Offset'] = 0.0
 
-            method = self.raw.GetInstrumentMethod(1)
-
-            offset = findall(r'Isolation[ m/z ]*Offset\s*=*\s*(\S+)', method, flags=IGNORECASE)[0]
-
-            if (offset.lower() == 'off') | (offset.lower() == 'false') :
-                offset = 0.0
-
-        self.MetaData['Offset'] = float(offset)
+        self.flags['BoxCar'] = boxcar
 
         self.Initialized = True
 
@@ -275,6 +264,8 @@ def ExtractTriggerMass(self):
 
         scans = self.info.loc[(self.info['MSOrder'] == 2), 'ScanNum']
 
+        print(self.RawFile + ': Extracting parent peak masses')
+
         self.data['TriggerMass'] = OD((str(x), self.raw.GetScanEventForScanNumber(x).Reactions[0].PrecursorMass -
                                        self.MetaData['Offset']) for x in scans)
 
@@ -424,8 +415,12 @@ def get_out(scan):
 
             keys = ['MassRange[' + str(x.LowMass) + '-' + str(x.HighMass) + ']FillTime' for x in ranges]
 
+            print(keys)
+
             fill_times = self.data['MS1TrailerExtra'][str(scan)]['Multi Inject Info'][3:].split(',')
 
+            print(fill_times)
+
             return OD((keys[x], fill_times[x]) for x in range(len(keys)))
 
         print(self.RawFile + ': Extracting boxcar mass ranges and fill times')
@@ -2026,9 +2021,9 @@ def __del__(self):
 
 
 # define a function to be used in parallelism
-def func(msFile, reagents, mgf, interference, impurities, metrics, boxcar):
+def func(msFile, reagents, mgf, interference, impurities, metrics, boxcar, isolationOffset=None):
     filename = msFile[:-4] + '_QuantData.txt'
-    data = RawQuant(msFile, disable_bar=True)
+    data = RawQuant(msFile, disable_bar=True, isolationOffset=isolationOffset)
 
     if boxcar:
         data.SetAsBoxcar()

RawQuant/__main__.py

@@ -160,7 +160,7 @@
                 'Number of CPU cores to be used when processing multiple files.\n'+
                 'If left blank a single core will be used.\n ')
 
-        quant.add_argument('-b', '--boxcar', help=
+        quant.add_argument('-b', '--boxcar', action='store_true', help=
                 'Indicates that the rawfile is from a boxcar experiment and the program'
                 'should look for multi-injection data.')
 
@@ -201,6 +201,9 @@
                 '>python -m RawQuant quant -f rawFile.raw -r TMT0 -mgf -mco 128\n' +
                 'cuts off all MS2 ions < m/z 128 when making the mgf file.')
 
+        quant.add_argument('-offset', '--isolation_window_offset', help=
+                'Specify the offset of the isolation window, if there was one.')
+
         ### Examples subparser section ###
 
         examples.add_argument('-m','--multiple', action='store_true', help =
@@ -267,6 +270,9 @@
         '>python -m RawQuant parse -f rawFile.raw -o 0 -mgf -mco 128\n' +
         'cuts off all MS2 ions < m/z 128 when making the mgf file.')
 
+        parse.add_argument('-offset', '--isolation_window_offset', help=
+        'Specify the offset of the isolation window, if there was one.')
+
         args = parser.parse_args()
 
     else:
@@ -712,7 +718,8 @@ def __init__(self):
         for msFile in files:
 
             filename = msFile[:-4]+'_ParseData.txt'
-            data = RawQuant(msFile,disable_bar=suppress_bar)
+            data = RawQuant(msFile, disable_bar=suppress_bar, isolationOffset=args.isolation_window_offset,
+                            boxcar=args.boxcar)
 
             if args.boxcar:
 
@@ -758,7 +765,7 @@ def __init__(self):
 
         elif args.multiple is not None:
 
-            files = np.loadtxt(args.multiple,dtype=str).tolist()
+            files = np.loadtxt(args.multiple, dtype=str).tolist()
 
         elif args.directory is not None:
 
@@ -822,7 +829,8 @@ def __init__(self):
             for msFile in files:
 
                 filename = msFile[:-4]+'_QuantData.txt'
-                data = RawQuant(msFile,order=order,disable_bar=suppress_bar)
+                data = RawQuant(msFile, order=order, disable_bar=suppress_bar, boxcar=args.boxcar,
+                                isolationOffset=args.isolation_window_offset)
 
                 if args.boxcar:
                     data.SetAsBoxcar()
@@ -841,7 +849,7 @@ def __init__(self):
                     data.GenerateCorrectionMatrix()
                     data.CorrectImpurities()
 
-                data.SaveData(filename = filename)
+                data.SaveData(filename=filename)
 
                 if args.generate_mgf:
 
@@ -869,4 +877,5 @@ def __init__(self):
 
             Parallel(n_jobs=num_cores)(delayed(func)(msFile=msFile, reagents=reagents, mgf=args.generate_mgf,
                                                      interference=args.quantify_interference, impurities=impurities,
-                                                     metrics=args.metrics, boxcar=args.boxcar) for msFile in files)
+                                                     metrics=args.metrics, boxcar=args.boxcar,
+                                                     isolationOffset=args.isolation_window_offset) for msFile in files)