def LabelMe(self):
Handle = open(self.InputFilePath, "rb")
Dymo = Label.LabelClass()
Count = 0
GoodScoreCount = 0
WrongChargeCount = 0
ScoredWorseCount = 0
for Line in Handle.xreadlines():
if Line[0] == "#":
self.Columns.initializeHeaders(Line)
continue
if not Line.strip():
continue
Bits = list(Line.strip().split("\t"))
#Charge = int (Bits[self.Columns.Charge]) I don't thin I need this anymore
Count += 1
Annotation = Bits[self.Columns.getIndex("Annotation")]
#print "Annotation :%s:"%Annotation
FileName = Bits[self.Columns.getIndex("SpectrumFile")]
Scan = int(Bits[self.Columns.getIndex("Scan#")])
if not self.InspectFormat:
FileNameMinusPath = os.path.split(FileName)[1]
(FullPathDummy,
ByteOffset) = self.ScanOffset[(FileNameMinusPath, Scan)]
#print (FullPathDummy, ByteOffset)
#continue
else:
ByteOffset = int(Bits[self.Columns.getIndex("SpecFilePos")])
(Path, File) = os.path.split(FileName)
FileName = os.path.join(self.MZXMLDir, File)
VerboseFileName = "%s.%s.%s.verbose.txt" % (File, Scan,
Annotation[2:-2])
ImageFileName = "%s.%s.%s.png" % (File, Scan, Annotation[2:-2])
VerboseFilePath = os.path.join(self.LabeledAnnotationsDir,
VerboseFileName)
ImageFilePath = os.path.join(self.LabeledAnnotationsDir,
ImageFileName)
## as we've got a single Dymo object, we must be passing in full args list
## -p to suppress the image popup, and -P for the PLS score
Args = " -r %s -b %d -a %s -v %s -w %s -p -P" % (
FileName, ByteOffset, Annotation, VerboseFilePath,
ImageFilePath)
ArgsList = Args.split()
#print "Parsing Results for %s, scan %s, charge %s"%(FileName, Scan, Charge)
#print "Args: %s"%Args
Dymo.ParseCommandLine(ArgsList)
Dymo.Main()
Handle.close()
def WritePeptideLine(self, File, IntervalStr, ProteinID, SpectrumIndex,
Peptide, TotalHitCount):
Dir = os.path.split(self.SummaryPagePath)[0]
Annotation = Peptide.GetModdedName()
SpecFileName = Peptide.SpectrumFilePath.replace("/",
"\\").split("\\")[-1]
if self.GenerateSpectrumImagesFlag:
ImageFileName = "%s.%s.png" % (Annotation, SpectrumIndex)
ImageFilePath = os.path.join(Dir, ImageFileName)
Maker = MakeImage.MSImageMaker()
MSpectrum = MSSpectrum.SpectrumClass()
Path = self.GetSpectrumPath(Peptide.SpectrumFilePath,
self.MZXMLPath)
FileName = "%s:%s" % (Path, Peptide.SpectrumFilePos)
try:
#SpectrumFile = Label.OpenAndSeekFile(FileName)
#print FileName
#MSpectrum.ReadPeaksFromFile(SpectrumFile, FileName)
#MSpectrum.RankPeaksByIntensity()
#SpectrumFile.close()
#Label.LabelSpectrum(MSpectrum, Peptide)
#Maker.ConvertSpectrumToImage(MSpectrum, ImageFilePath, Peptide, Width = 500, Height = 380)
Args = " -r %s -b %d -a %s -w %s -p" % (
Path, int(
Peptide.SpectrumFilePos), Annotation, ImageFilePath)
ArgsList = Args.split()
#print "Parsing Results for %s, scan %s"%(FileName, Scan)
Dymo = Label.LabelClass()
Dymo.ParseCommandLine(ArgsList)
#Dymo.LoadModel(0, Dymo.PeptideHasPhosphorylation)
Dymo.Main()
except:
traceback.print_exc()
File.write(
"<tr><td>%s</td><td>%s</td><td><a href=\"%s\">%s</td><td>%s</td><td>%s</td>"
%
(IntervalStr, TotalHitCount, ImageFileName,
Peptide.GetFullModdedName(), Peptide.PValue, Peptide.MQScore))
File.write("<td>%s</td><td>%s</td></tr>\n" %
(SpecFileName, Peptide.ScanNumber))
else:
File.write(
"<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td>" %
(IntervalStr, TotalHitCount, Peptide.GetFullModdedName(),
Peptide.PValue, Peptide.MQScore))
File.write("<td>%s</td><td>%s</td></tr>\n" %
(SpecFileName, Peptide.ScanNumber))