def exeCompassXport(self, file2Convert, newFileName = None):
t1 = time.clock()
self.cmdOut = ['CompassXport']
filetype = str(self.outputFile).split('.')[-1]
if filetype == 'mzXML':
self.cmdOut.append(' -mode 0 ')
elif filetype == 'None':
self.cmdOut.append(' -mode 0 ')
elif filetype == 'mzDATA':
self.cmdOut.append(' -mode 1 ')
inputFile = ' -a '+file2Convert
self.cmdOut.append(inputFile)
if newFileName != None:
if filetype == 'None':
newFileName+='.mzXML'
newPath = os.path.join(str(self.fileData), newFileName)
elif filetype != 'None' and self.useSingleFile == False:
newFileName += '.mzXML'
newPath = os.path.join(str(self.outputFile), newFileName)
else:
newPath=str(self.outputFile)
else:
newFileName='analysis.mzXML'
self.dir = os.path.dirname(str(self.fileData))
newPath = os.path.join(self.dir, newFileName)
#this small code block writes a peak list to a csv file
try:
peakList = brukerPeakList(file2Convert)#used for csv
peakList.saveCSV(os.path.splitext(newPath)[0])#used for csv
except:
print "Error converting Bruker peaklist for %s"%file2Convert
outFile = ' -o '+newPath
self.cmdOut.append(outFile)
cmdStr = ''
for item in self.cmdOut:
cmdStr += item
cmdStr +='\n'
try:
subHandle = sub.Popen(cmdStr, bufsize = 0, shell = True, stdout=sub.PIPE, stderr=sub.PIPE, stdin = sub.PIPE)
self.outMsg = subHandle.stdout.read()
self.errMsg = subHandle.stderr.read()
subHandle.stderr.close()
subHandle.stdout.close()
subHandle.stdin.close()
self.retCode = subHandle.wait()
########BEGIN CONVERT TO CSV
if self.writeCSV:
mzr = MzR(newPath)
mzr.saveCSV(os.path.splitext(newPath)[0])
###############################
t2 = time.clock()
runTime= '%s sec\n\n'%(t2-t1)
if self.retCode != 0:
msg = self.outMsg+'\n'+self.errMsg
fileupdate = '%d of %d Finished\n'%(self.curFileNum+1, self.totalFiles)
msg +=fileupdate
msg += runTime
return msg
else:
msg = self.outMsg+'\n'+self.errMsg
fileupdate = '%d of %d Finished\n'%(self.curFileNum+1, self.totalFiles)
msg +=fileupdate
msg += runTime
return msg
except:
print cmdStr
raise
def exeCompassXport(self, file2Convert, newFileName = None):
self.cmdOut = ['CompassXport']
filetype = str(self.outputFile).split('.')[-1]
if filetype == 'mzXML':
self.cmdOut.append(' -mode 0 ')
elif filetype == 'None':
self.cmdOut.append(' -mode 0 ')
elif filetype == 'mzDATA':
self.cmdOut.append(' -mode 1 ')
inputFile = ' -a '+file2Convert
self.cmdOut.append(inputFile)
if newFileName != None:
if filetype == 'None':
newFileName+='.mzXML'
newPath = os.path.join(str(self.fileData), newFileName)
elif filetype != 'None' and self.useSingleFile == False:
newFileName += '.mzXML'
newPath = os.path.join(str(self.outputFile), newFileName)
else:
newPath=str(self.outputFile)
else:
newFileName='analysis.mzXML'
self.dir = os.path.dirname(str(self.fileData))
newPath = os.path.join(self.dir, newFileName)
#this small code block writes a peak list to a csv file
peakList = brukerPeakList(file2Convert)#used for csv
peakList.saveCSV(os.path.splitext(newPath)[0])#used for csv
outFile = ' -o '+newPath
self.cmdOut.append(outFile)
cmdStr = ''
for item in self.cmdOut:
cmdStr += item
cmdStr +='\n'
try:
subHandle = sub.Popen(cmdStr, bufsize = 0, shell = True, stdout=sub.PIPE, stderr=sub.PIPE, stdin = sub.PIPE)
self.outMsg = subHandle.stdout.read()
self.errMsg = subHandle.stderr.read()
subHandle.stderr.close()
subHandle.stdout.close()
subHandle.stdin.close()
self.retCode = subHandle.wait()
if self.retCode != 0:
self.outputTE.insertPlainText(QtCore.QString(cmdStr))
msg = self.outMsg+'\n'+self.errMsg
self.outputTE.insertPlainText(QtCore.QString(msg))
self.outputTE.update()
else:
msg = self.outMsg+'\n'+self.errMsg
self.outputTE.insertPlainText(QtCore.QString(msg))
self.outputTE.update()
except:
print cmdStr
raise