def loadPlugins(self, pluginFolder):
os.chdir(getMainDir())
pluginModulePath = pluginFolder.replace('/', '.')
if runningExecutable():
if platform.system() == 'Windows':
# windows plugin folder
pluginFolder = 'library/' + pluginFolder
else:
# os x plugin folder
pluginFolder = './lib/python2.6/site-packages/' + pluginFolder
dict = {}
for filename in os.listdir(pluginFolder):
if os.path.isdir(os.path.join(pluginFolder, filename)):
continue
extension = filename[filename.rfind('.') + 1:len(filename)]
if extension == 'py' and filename != '__init__.py':
pluginModule = filename[0:filename.rfind('.')]
theModule = __import__(pluginModulePath + pluginModule,
fromlist='*')
theClass = getattr(theModule, pluginModule)
theObject = theClass(self.preferences)
dict[theObject.name] = theObject
return dict
def loadPlugins(self, pluginFolder):
os.chdir(getMainDir())
pluginModulePath = pluginFolder.replace('/', '.')
if runningExecutable():
if platform.system() == 'Windows':
# windows plugin folder
pluginFolder = 'library/' + pluginFolder
else:
# os x plugin folder
pluginFolder = './lib/python2.6/site-packages/' + pluginFolder
dict = {}
for filename in os.listdir(pluginFolder):
if os.path.isdir(os.path.join (pluginFolder, filename)):
continue
extension = filename[filename.rfind('.')+1:len(filename)]
if extension == 'py' and filename != '__init__.py':
pluginModule = filename[0:filename.rfind('.')]
theModule = __import__(pluginModulePath + pluginModule, fromlist='*')
theClass = getattr(theModule, pluginModule)
theObject = theClass(self.preferences)
dict[theObject.name] = theObject
return dict
def loadPlots(self, preferences, pluginFolder):
os.chdir(getMainDir())
pluginModulePath = pluginFolder.replace('/', '.')
if runningExecutable():
if platform.system() == 'Windows':
# windows plugin folder
pluginFolder = 'library/' + pluginFolder
else:
# os x plugin folder
pluginFolder = './lib/python2.6/site-packages/' + pluginFolder
for filename in os.listdir(pluginFolder):
if os.path.isdir(os.path.join (pluginFolder, filename)):
continue
extension = filename[filename.rfind('.')+1:len(filename)]
if extension == 'py' and filename != '__init__.py':
pluginModule = filename[0:filename.rfind('.')]
theModule = __import__(pluginModulePath + pluginModule, fromlist='*')
theClass = getattr(theModule, pluginModule)
plot = theClass(preferences)
self.plotClassDict[plot.name] = theClass
self.plotDict[plot.name] = plot
exploratoryPlots = []
statisticalPlots = []
for key in self.plotDict:
if self.plotDict[key].type == 'Exploratory':
exploratoryPlots.append(key)
else:
statisticalPlots.append(key)
exploratoryPlots.sort(lambda a,b:cmp(a.upper(), b.upper()))
statisticalPlots.sort(lambda a,b:cmp(a.upper(), b.upper()))
for plotName in exploratoryPlots:
self.cboPlots.addItem(plotName)
self.cboPlots.insertSeparator(self.cboPlots.count())
for plotName in statisticalPlots:
self.cboPlots.addItem(plotName)
self.display(self.defaultPlot, None, None)
self.cboPlots.setCurrentIndex(self.cboPlots.findText(self.defaultPlot))
filename, line, dummy, dummy = traceback.extract_tb(exc_traceback).pop()
filename = os.path.basename(filename)
error = "%s: %s" % (exc_type.__name__, exc_value)
QtGui.QMessageBox.critical(
mainWindow, "Unknown error...",
"<center>An error has occured. This is most likely a bug in STAMP. The error is:<br/><br/>"
+ "<b><i>%s</i></b><br/>" % error +
"It occured at <b>line %d</b> of file <b>%s</b>.<br/>" %
(line, filename) + "</center>")
if __name__ == "__main__":
# change the current working directory
os.chdir(getMainDir())
# initialize preferences
preferences = {}
preferences['Pseudocount'] = 0.5
preferences['Truncate feature names'] = True
preferences['Length of truncated feature names'] = 50
preferences['Sample 1 colour'] = QtGui.QColor(0, 0, 255)
preferences['Sample 2 colour'] = QtGui.QColor(255, 127, 0)
preferences['Selected exploratory features'] = []
preferences['Selected statistical features'] = []
preferences['Executable directory'] = sys.path[0]
if len(sys.argv) == 2 and sys.argv[1].startswith("--macapp"):
del sys.argv[1]
def appendCategories(self, inputFile, multiCogTreatment, outputFile,
preferences):
fin = open(getMainDir() + '/data/fun.txt', 'U')
funcData = fin.readlines()
fin.close()
# get COG hierarchy information
funcDict = {}
for line in funcData:
line = line.strip()
if len(line) == 0:
continue
if ':' in line:
code = line[0]
categoryName = line[2:]
funcDict[code] = [curClass, categoryName]
else:
# new functional classes
curClass = line
# get COG category for each COG
fin = open(getMainDir() + '/data/whog.txt', 'U')
cogData = fin.readlines()
fin.close()
cogDict = {}
for line in cogData:
if '[' in line:
# need to parse a new COG
code = line[line.find('[') + 1:line.find(']')]
cogIndex = line.find('COG')
cogId = line[cogIndex:cogIndex + 7]
cogDict[cogId] = code
# modify input file
fin = open(inputFile, 'U')
inputData = fin.readlines()
fin.close()
fout = open(outputFile, 'w')
# write out header information
headers = inputData[0].strip()
headers = headers.split('\t')
fout.write('COG classes' + '\t' + 'COG category names' + '\t' +
'COG category codes' + '\t' + 'COG annotations' + '\t' +
'COG IDs')
for i in xrange(2, len(headers)):
fout.write('\t' + headers[i])
fout.write('\n')
# write out each row
for i in xrange(1, len(inputData)):
line = inputData[i].strip()
lineSplit = line.split('\t')
cogId = lineSplit[0]
cogAnnotation = lineSplit[1]
cogCode = cogDict[cogId]
if multiCogTreatment == 'Treat multi-code COGs as features':
cogClass, cogCategoryName = funcDict.get(
cogCode, [cogCode, cogCode])
fout.write(cogClass + '\t' + cogCategoryName + '\t' + cogCode +
'\t' + cogAnnotation + '\t' + cogId)
for j in xrange(2, len(lineSplit)):
fout.write('\t' + lineSplit[j])
fout.write('\n')
elif multiCogTreatment == 'Assign sequence to each COG code':
for ch in cogCode:
cogClass, cogCategoryName = funcDict.get(
ch, [cogCode, cogCode])
fout.write(cogClass + '\t' + cogCategoryName + '\t' + ch +
'\t' + cogAnnotation + '\t' + cogId)
for j in xrange(2, len(lineSplit)):
fout.write('\t' + lineSplit[j])
fout.write('\n')
fout.close()
#=======================================================================
def saveSummaryTable(self, filename, statsTestResults):
tableData, tableHeadings = statsTestResults.tableData(True)
tableData = SortTableStrCol(tableData, 0)
fout = open(filename, "w")
for heading in tableHeadings:
fout.write(heading + "\t")
fout.write("\n")
for row in tableData:
for entry in row:
fout.write(str(entry) + "\t")
fout.write("\n")
fout.close()
if __name__ == "__main__":
# change the current working directory
os.chdir(getMainDir())
# initialize preferences
preferences = {}
preferences["Pseudocount"] = 0.5
preferences["Executable directory"] = sys.path[0]
commandLineParser = CommandLineParser(preferences)
commandLineParser.run()
sys.exit()
def appendCategories(self, inputFile, multiCogTreatment, outputFile, preferences):
fin = open(getMainDir() + '/data/fun.txt', 'U')
funcData = fin.readlines()
fin.close()
# get COG hierarchy information
funcDict = {}
for line in funcData:
line = line.strip()
if len(line) == 0:
continue
if ':' in line:
code = line[0]
categoryName = line[2:]
funcDict[code] = [curClass, categoryName]
else:
# new functional classes
curClass = line
# get COG category for each COG
fin = open(getMainDir() + '/data/whog.txt', 'U')
cogData = fin.readlines()
fin.close()
cogDict = {}
for line in cogData:
if '[' in line:
# need to parse a new COG
code = line[line.find('[')+1:line.find(']')]
cogIndex = line.find('COG')
cogId = line[cogIndex:cogIndex+7]
cogDict[cogId] = code
# modify input file
fin = open(inputFile, 'U')
inputData = fin.readlines()
fin.close()
fout = open(outputFile, 'w')
# write out header information
headers = inputData[0].strip()
headers = headers.split('\t')
fout.write('COG classes' + '\t' + 'COG category names' + '\t' + 'COG category codes'
+ '\t' + 'COG annotations' + '\t' + 'COG IDs')
for i in xrange(2,len(headers)):
fout.write('\t' + headers[i])
fout.write('\n')
# write out each row
for i in xrange(1, len(inputData)):
line = inputData[i].strip()
lineSplit = line.split('\t')
cogId = lineSplit[0]
cogAnnotation = lineSplit[1]
cogCode = cogDict[cogId]
if multiCogTreatment == 'Treat multi-code COGs as features':
cogClass, cogCategoryName = funcDict.get(cogCode, [cogCode, cogCode])
fout.write(cogClass + '\t' + cogCategoryName + '\t' + cogCode + '\t' + cogAnnotation + '\t' + cogId)
for j in xrange(2, len(lineSplit)):
fout.write('\t' + lineSplit[j])
fout.write('\n')
elif multiCogTreatment == 'Assign sequence to each COG code':
for ch in cogCode:
cogClass, cogCategoryName = funcDict.get(ch, [cogCode, cogCode])
fout.write(cogClass + '\t' + cogCategoryName + '\t' + ch + '\t' + cogAnnotation + '\t' + cogId)
for j in xrange(2, len(lineSplit)):
fout.write('\t' + lineSplit[j])
fout.write('\n')
fout.close()