def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileRITADlg()
self.ui.setupUi(self)
self.preferences = preferences
self.centerWindow()
QtCore.QObject.connect(self.ui.btnLoadProfiles,
QtCore.SIGNAL("clicked()"), self.loadProfiles)
QtCore.QObject.connect(self.ui.btnCreateProfile,
QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"),
self.accept)
self.selectedFiles = []
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileRITADlg()
self.ui.setupUi(self)
self.preferences = preferences
self.centerWindow()
QtCore.QObject.connect(self.ui.btnLoadProfiles, QtCore.SIGNAL("clicked()"), self.loadProfiles)
QtCore.QObject.connect(self.ui.btnCreateProfile, QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"), self.accept)
self.selectedFiles = []
class CreateProfileRITADlg(QtGui.QDialog):
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileRITADlg()
self.ui.setupUi(self)
self.preferences = preferences
self.centerWindow()
QtCore.QObject.connect(self.ui.btnLoadProfiles, QtCore.SIGNAL("clicked()"), self.loadProfiles)
QtCore.QObject.connect(self.ui.btnCreateProfile, QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"), self.accept)
self.selectedFiles = []
def loadProfiles(self):
selectedFiles = QtGui.QFileDialog.getOpenFileNames(self, 'Load profiles', self.preferences['Last directory'], 'RITA profiles (*.txt);;All files (*.*)')
if len(selectedFiles) > 0:
self.preferences['Last directory'] = selectedFiles[0][0:selectedFiles[0].lastIndexOf('/')]
for file in selectedFiles:
self.selectedFiles.append(str(file))
self.ui.lstSelectedProfiles.addItem(file)
self.ui.btnCreateProfile.setEnabled(True)
def createProfile(self):
# get filename to save STAMP profile to
stampFilename = QtGui.QFileDialog.getSaveFileName(self, 'Save STAMP profile...', self.preferences['Last directory'], 'STAMP profile file(*.spf);;All files(*.*)')
if stampFilename == '':
return
# get checked groups
checkedGroups = []
if self.ui.chkNB_DBLASTN.isChecked():
checkedGroups.append('NB and D-BLASTN')
if self.ui.chkDBLASTN.isChecked():
checkedGroups.append('D-BLASTN ratio')
if self.ui.chkNB_BLASTN.isChecked():
checkedGroups.append('NB and BLASTN')
if self.ui.chkBLASTN.isChecked():
checkedGroups.append('BLASTN ratio')
if self.ui.chkNB_BLASTX.isChecked():
checkedGroups.append('NB and BLASTX')
if self.ui.chkBLASTX.isChecked():
checkedGroups.append('BLASTX ratio')
if self.ui.chkNB.isChecked():
checkedGroups.append('NB ratio')
# get profile information from each file
profileDict = {}
profileIndex = 0
sampleNames = []
mostSpecificRankIndex = 0
ranks = ['DOMAIN', 'PHYLUM', 'CLASS', 'ORDER', 'FAMILY', 'GENUS', 'SPECIES']
for file in self.selectedFiles:
fin = open(file, 'U')
data = map(string.strip, fin.readlines())
fin.close()
sampleName = file[file.rfind('/')+1:file.find('.')]
if sampleName.find('_') != -1:
sampleName = sampleName[sampleName.find('_')+1:]
sampleNames.append(sampleName)
# add profile info
categories = set([])
for i in xrange(1, len(data)):
line = data[i]
if line == "":
continue # skip blank lines
lineSplit = line.split('\t')
groupName = lineSplit[2]
rank = lineSplit[3]
if groupName not in checkedGroups:
continue
if ranks.index(rank) > mostSpecificRankIndex:
mostSpecificRankIndex = ranks.index(rank)
hierarchy = ';'.join(lineSplit[4:])
row = profileDict.get(hierarchy, None)
if row == None:
row = ProfileRow()
row.countData = [0] * len(self.selectedFiles)
row.hierarchy = hierarchy
profileDict[hierarchy] = row
row.countData[profileIndex] += 1
profileIndex += 1
# write out STAMP profile
try:
fout = open(stampFilename, 'w')
except IOError:
QtGui.QMessageBox.information(self, 'Failed to save STAMP profile', 'Write permission for file denied.', QtGui.QMessageBox.Ok)
return
mostSpecificRank = ranks[mostSpecificRankIndex]
if mostSpecificRank == 'DOMAIN':
fout.write('Domain')
elif mostSpecificRank == 'PHYLUM':
fout.write('Domain\tPhylum')
elif mostSpecificRank == 'CLASS':
fout.write('Domain\tPhylum\tClass')
elif mostSpecificRank == 'ORDER':
fout.write('Domain\tPhylum\tClass\tOrder')
elif mostSpecificRank == 'FAMILY':
fout.write('Domain\tPhylum\tClass\tOrder\tFamily')
elif mostSpecificRank == 'GENUS':
fout.write('Domain\tPhylum\tClass\tOrder\tFamily\tGenus')
elif mostSpecificRank == 'SPECIES':
fout.write('Domain\tPhylum\tClass\tOrder\tFamily\tGenus\tSpecies')
for sampleName in sampleNames:
fout.write('\t' + sampleName)
fout.write('\n')
for key in profileDict.keys():
row = profileDict[key]
hierarchy = row.hierarchy.split(';')
for h in xrange(len(hierarchy)-1, -1, -1):
fout.write(hierarchy[h] + '\t')
for i in xrange(0, mostSpecificRankIndex-len(hierarchy)+1):
fout.write('Unclassified' + '\t')
fout.write(str(row.countData[0]))
for c in row.countData[1:]:
fout.write('\t' + str(c))
fout.write('\n')
fout.close()
self.accept()
def centerWindow(self):
screen = QtGui.QDesktopWidget().screenGeometry()
size = self.geometry()
self.move((screen.width()-size.width())/2, (screen.height()-size.height())/2)
class CreateProfileRITADlg(QtGui.QDialog):
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileRITADlg()
self.ui.setupUi(self)
self.preferences = preferences
self.centerWindow()
QtCore.QObject.connect(self.ui.btnLoadProfiles,
QtCore.SIGNAL("clicked()"), self.loadProfiles)
QtCore.QObject.connect(self.ui.btnCreateProfile,
QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"),
self.accept)
self.selectedFiles = []
def loadProfiles(self):
selectedFiles = QtGui.QFileDialog.getOpenFileNames(
self, 'Load profiles', self.preferences['Last directory'],
'RITA profiles (*.txt);;All files (*.*)')
if len(selectedFiles) > 0:
self.preferences['Last directory'] = selectedFiles[0][
0:selectedFiles[0].lastIndexOf('/')]
for file in selectedFiles:
self.selectedFiles.append(str(file))
self.ui.lstSelectedProfiles.addItem(file)
self.ui.btnCreateProfile.setEnabled(True)
def createProfile(self):
# get filename to save STAMP profile to
stampFilename = QtGui.QFileDialog.getSaveFileName(
self, 'Save STAMP profile...', self.preferences['Last directory'],
'STAMP profile file(*.spf);;All files(*.*)')
if stampFilename == '':
return
# get checked groups
checkedGroups = []
if self.ui.chkNB_DBLASTN.isChecked():
checkedGroups.append('NB and D-BLASTN')
if self.ui.chkDBLASTN.isChecked():
checkedGroups.append('D-BLASTN ratio')
if self.ui.chkNB_BLASTN.isChecked():
checkedGroups.append('NB and BLASTN')
if self.ui.chkBLASTN.isChecked():
checkedGroups.append('BLASTN ratio')
if self.ui.chkNB_BLASTX.isChecked():
checkedGroups.append('NB and BLASTX')
if self.ui.chkBLASTX.isChecked():
checkedGroups.append('BLASTX ratio')
if self.ui.chkNB.isChecked():
checkedGroups.append('NB ratio')
# get profile information from each file
profileDict = {}
profileIndex = 0
sampleNames = []
mostSpecificRankIndex = 0
ranks = [
'DOMAIN', 'PHYLUM', 'CLASS', 'ORDER', 'FAMILY', 'GENUS', 'SPECIES'
]
for file in self.selectedFiles:
fin = open(file, 'U')
data = map(string.strip, fin.readlines())
fin.close()
sampleName = file[file.rfind('/') + 1:file.find('.')]
if sampleName.find('_') != -1:
sampleName = sampleName[sampleName.find('_') + 1:]
sampleNames.append(sampleName)
# add profile info
categories = set([])
for i in xrange(1, len(data)):
line = data[i]
if line == "":
continue # skip blank lines
lineSplit = line.split('\t')
groupName = lineSplit[2]
rank = lineSplit[3]
if groupName not in checkedGroups:
continue
if ranks.index(rank) > mostSpecificRankIndex:
mostSpecificRankIndex = ranks.index(rank)
hierarchy = ';'.join(lineSplit[4:])
row = profileDict.get(hierarchy, None)
if row == None:
row = ProfileRow()
row.countData = [0] * len(self.selectedFiles)
row.hierarchy = hierarchy
profileDict[hierarchy] = row
row.countData[profileIndex] += 1
profileIndex += 1
# write out STAMP profile
try:
fout = open(stampFilename, 'w')
except IOError:
QtGui.QMessageBox.information(self, 'Failed to save STAMP profile',
'Write permission for file denied.',
QtGui.QMessageBox.Ok)
return
mostSpecificRank = ranks[mostSpecificRankIndex]
if mostSpecificRank == 'DOMAIN':
fout.write('Domain')
elif mostSpecificRank == 'PHYLUM':
fout.write('Domain\tPhylum')
elif mostSpecificRank == 'CLASS':
fout.write('Domain\tPhylum\tClass')
elif mostSpecificRank == 'ORDER':
fout.write('Domain\tPhylum\tClass\tOrder')
elif mostSpecificRank == 'FAMILY':
fout.write('Domain\tPhylum\tClass\tOrder\tFamily')
elif mostSpecificRank == 'GENUS':
fout.write('Domain\tPhylum\tClass\tOrder\tFamily\tGenus')
elif mostSpecificRank == 'SPECIES':
fout.write('Domain\tPhylum\tClass\tOrder\tFamily\tGenus\tSpecies')
for sampleName in sampleNames:
fout.write('\t' + sampleName)
fout.write('\n')
for key in profileDict.keys():
row = profileDict[key]
hierarchy = row.hierarchy.split(';')
for h in xrange(len(hierarchy) - 1, -1, -1):
fout.write(hierarchy[h] + '\t')
for i in xrange(0, mostSpecificRankIndex - len(hierarchy) + 1):
fout.write('Unclassified' + '\t')
fout.write(str(row.countData[0]))
for c in row.countData[1:]:
fout.write('\t' + str(c))
fout.write('\n')
fout.close()
self.accept()
def centerWindow(self):
screen = QtGui.QDesktopWidget().screenGeometry()
size = self.geometry()
self.move((screen.width() - size.width()) / 2,
(screen.height() - size.height()) / 2)