def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileMgRastDlg()
self.ui.setupUi(self)
self.centerWindow()
self.preferences = preferences
QtCore.QObject.connect(self.ui.btnLoadProfiles, QtCore.SIGNAL("clicked()"), self.loadProfiles)
QtCore.QObject.connect(self.ui.btnCustomizeHeadings, QtCore.SIGNAL("clicked()"), self.customizeHeadings)
QtCore.QObject.connect(self.ui.btnCreateProfile, QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"), self.accept)
self.headings = []
self.selectedFile = ''
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileMgRastDlg()
self.ui.setupUi(self)
self.centerWindow()
self.preferences = preferences
QtCore.QObject.connect(self.ui.btnLoadProfiles, QtCore.SIGNAL("clicked()"), self.loadProfiles)
QtCore.QObject.connect(self.ui.btnCustomizeHeadings, QtCore.SIGNAL("clicked()"), self.customizeHeadings)
QtCore.QObject.connect(self.ui.btnCreateProfile, QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"), self.accept)
self.headings = []
self.selectedFile = ''
class CreateProfileMgRastDlg(QtGui.QDialog):
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileMgRastDlg()
self.ui.setupUi(self)
self.centerWindow()
self.preferences = preferences
QtCore.QObject.connect(self.ui.btnLoadProfiles, QtCore.SIGNAL("clicked()"), self.loadProfiles)
QtCore.QObject.connect(self.ui.btnCustomizeHeadings, QtCore.SIGNAL("clicked()"), self.customizeHeadings)
QtCore.QObject.connect(self.ui.btnCreateProfile, QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"), self.accept)
self.headings = []
self.selectedFile = ''
def loadProfiles(self):
self.selectedFile = QtGui.QFileDialog.getOpenFileName(self, 'Load profile', self.preferences['Last directory'], 'MG-RAST profile (*.tsv);;All files (*.*)')
if self.selectedFile != '':
self.preferences['Last directory'] = self.selectedFile[0:self.selectedFile.lastIndexOf('/')]
# read profile information from file
fin = open(self.selectedFile, 'U')
self.data = map(string.strip, fin.readlines())
fin.close()
# get header data
self.header = self.data[0].split('\t')
if self.header[0].strip() != 'metagenome':
QtGui.QMessageBox.information(self, 'Failed to parse MG-RAST profile', "This file does not appear to be a valid MG-RAST profile as it does not begin with a 'metagenome' column.", QtGui.QMessageBox.Ok)
return
if 'abundance' not in self.header:
QtGui.QMessageBox.information(self, 'Failed to parse MG-RAST profile', "This file does not appear to be a valid MG-RAST profile as it does not contain an 'abundance' column.", QtGui.QMessageBox.Ok)
return
if self.header[1] != 'level 1' and self.header[1] != 'source' and self.header[1] != 'domain':
QtGui.QMessageBox.information(self, 'Failed to parse MG-RAST profile', "This file does not appear to be a valid MG-RAST profile as the second column is not 'level 1', 'source', or 'domain'.", QtGui.QMessageBox.Ok)
return
if self.header[1] == 'level 1' or self.header[1] == 'domain':
self.startIndex = 1
else:
self.startIndex = 2
for i in xrange(self.startIndex, self.header.index('abundance')):
self.headings.append(self.header[i])
for i in xrange(0, 8-len(self.headings)):
self.headings.append('')
self.ui.btnCustomizeHeadings.setEnabled(True)
self.ui.btnCreateProfile.setEnabled(True)
def customizeHeadings(self):
customizeHeadingsDlg = CustomizeHeadingsDlg(self)
numHeadings = len(self.headings)
if '' in self.headings:
numHeadings = self.headings.index('')
customizeHeadingsDlg.ui.txtInfo.setText('This MG-RAST profiles consists of ' + str(numHeadings) + ' hierarchical levels.')
customizeHeadingsDlg.ui.txtLevel1.setText(self.headings[0])
customizeHeadingsDlg.ui.txtLevel2.setText(self.headings[1])
customizeHeadingsDlg.ui.txtLevel3.setText(self.headings[2])
customizeHeadingsDlg.ui.txtLevel4.setText(self.headings[3])
customizeHeadingsDlg.ui.txtLevel5.setText(self.headings[4])
customizeHeadingsDlg.ui.txtLevel6.setText(self.headings[5])
customizeHeadingsDlg.ui.txtLevel7.setText(self.headings[6])
customizeHeadingsDlg.ui.txtLevel8.setText(self.headings[7])
if customizeHeadingsDlg.exec_() == QtGui.QDialog.Accepted:
self.headings[0] = customizeHeadingsDlg.ui.txtLevel1.text()
self.headings[1] = customizeHeadingsDlg.ui.txtLevel2.text()
self.headings[2] = customizeHeadingsDlg.ui.txtLevel3.text()
self.headings[3] = customizeHeadingsDlg.ui.txtLevel4.text()
self.headings[4] = customizeHeadingsDlg.ui.txtLevel5.text()
self.headings[5] = customizeHeadingsDlg.ui.txtLevel6.text()
self.headings[6] = customizeHeadingsDlg.ui.txtLevel7.text()
self.headings[7] = customizeHeadingsDlg.ui.txtLevel8.text()
def createProfile(self):
splitCh = '\t'
# 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
self.preferences['Last directory'] = stampFilename[0:stampFilename.lastIndexOf('/')]
# set profile specific parsing information
hierarchyStartIndex = self.startIndex
dataIndex = self.header.index('abundance')
# determine samples in profile
sampleNames = []
for i in xrange(1, len(self.data)):
sampleId = self.data[i].split(splitCh)[0]
if sampleId not in sampleNames:
sampleNames.append(sampleId)
# add profile info
profileDict = {}
parentMap = {}
for i in xrange(1, dataIndex-hierarchyStartIndex):
parentMap[i] = {}
for i in xrange(1, len(self.data)):
if self.data[i] == "":
continue # skip blank lines
lineSplit = self.data[i].split(splitCh)
if len(lineSplit) <= dataIndex:
QtGui.QMessageBox.information(self, 'Unrecognized file format', 'Your file does not appear to be a valid MG-RAST profile.')
return
count = int(lineSplit[dataIndex])
hierarchy = lineSplit[hierarchyStartIndex:dataIndex]
# replace '-' categories with parent
for i in xrange(1, len(hierarchy)):
if hierarchy[i] == '-':
if self.header[1] == 'domain':
if 'Unclassified' not in hierarchy[i-1]:
hierarchy[i] = 'Unclassified ' + hierarchy[i-1]
else:
hierarchy[i] = hierarchy[i-1]
else:
hierarchy[i] = hierarchy[i-1]
# force MG-RAST profile to be strictly tree-like
for i in xrange(1, len(hierarchy)):
parent = '-'.join(hierarchy[0:i])
child = hierarchy[i]
currentParentMap = parentMap[i]
parentList = currentParentMap.get(child, [])
if parent not in parentList:
parentList.append(parent)
parentMap[i][child] = parentList
parentIndex = parentList.index(parent)
if parentIndex != 0:
newChild = child + ' - #' + str(parentIndex)
hierarchy[i] = newChild
# add to profile
sampleId = lineSplit[0]
profileIndex = sampleNames.index(sampleId)
row = profileDict.get(hierarchy[-1], None)
if row == None:
row = ProfileRow()
row.countData = [0] * len(sampleNames)
row.hierarchy = hierarchy
profileDict[hierarchy[-1]] = row
row.countData[profileIndex] += count
# 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
fout.write(self.headings[0])
for heading in self.headings[1:(dataIndex-hierarchyStartIndex)]:
fout.write('\t' + heading)
for sampleName in sampleNames:
fout.write('\t' + sampleName)
fout.write('\n')
for key in profileDict.keys():
row = profileDict[key]
for h in row.hierarchy:
fout.write(h + '\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 CreateProfileMgRastDlg(QtGui.QDialog):
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileMgRastDlg()
self.ui.setupUi(self)
self.centerWindow()
self.preferences = preferences
QtCore.QObject.connect(self.ui.btnLoadProfiles, QtCore.SIGNAL("clicked()"), self.loadProfiles)
QtCore.QObject.connect(self.ui.btnCustomizeHeadings, QtCore.SIGNAL("clicked()"), self.customizeHeadings)
QtCore.QObject.connect(self.ui.btnCreateProfile, QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"), self.accept)
self.headings = []
self.selectedFile = ''
def loadProfiles(self):
self.selectedFile = QtGui.QFileDialog.getOpenFileName(self, 'Load profile', self.preferences['Last directory'], 'MG-RAST profile (*.tsv);;All files (*.*)')
if self.selectedFile != '':
self.preferences['Last directory'] = self.selectedFile[0:self.selectedFile.lastIndexOf('/')]
# read profile information from file
fin = open(self.selectedFile, 'U')
self.data = map(string.strip, fin.readlines())
fin.close()
# get header data
self.header = self.data[0].split('\t')
if self.header[0].strip() != 'metagenome':
QtGui.QMessageBox.information(self, 'Failed to parse MG-RAST profile', "This file does not appear to be a valid MG-RAST profile as it does not begin with a 'metagenome' column.", QtGui.QMessageBox.Ok)
return
if 'abundance' not in self.header:
QtGui.QMessageBox.information(self, 'Failed to parse MG-RAST profile', "This file does not appear to be a valid MG-RAST profile as it does not contain an 'abundance' column.", QtGui.QMessageBox.Ok)
return
if self.header[1] != 'level 1' and self.header[1] != 'source' and self.header[1] != 'domain':
QtGui.QMessageBox.information(self, 'Failed to parse MG-RAST profile', "This file does not appear to be a valid MG-RAST profile as the second column is not 'level 1', 'source', or 'domain'.", QtGui.QMessageBox.Ok)
return
if self.header[1] == 'level 1' or self.header[1] == 'domain':
self.startIndex = 1
else:
self.startIndex = 2
for i in xrange(self.startIndex, self.header.index('abundance')):
self.headings.append(self.header[i])
for i in xrange(0, 8-len(self.headings)):
self.headings.append('')
self.ui.btnCustomizeHeadings.setEnabled(True)
self.ui.btnCreateProfile.setEnabled(True)
def customizeHeadings(self):
customizeHeadingsDlg = CustomizeHeadingsDlg(self)
customizeHeadingsDlg.ui.txtInfo.setText('This MG-RAST profiles consists of ' + str(self.headings.index('')) + ' hierarchical levels.')
customizeHeadingsDlg.ui.txtLevel1.setText(self.headings[0])
customizeHeadingsDlg.ui.txtLevel2.setText(self.headings[1])
customizeHeadingsDlg.ui.txtLevel3.setText(self.headings[2])
customizeHeadingsDlg.ui.txtLevel4.setText(self.headings[3])
customizeHeadingsDlg.ui.txtLevel5.setText(self.headings[4])
customizeHeadingsDlg.ui.txtLevel6.setText(self.headings[5])
customizeHeadingsDlg.ui.txtLevel7.setText(self.headings[6])
customizeHeadingsDlg.ui.txtLevel8.setText(self.headings[7])
if customizeHeadingsDlg.exec_() == QtGui.QDialog.Accepted:
self.headings[0] = customizeHeadingsDlg.ui.txtLevel1.text()
self.headings[1] = customizeHeadingsDlg.ui.txtLevel2.text()
self.headings[2] = customizeHeadingsDlg.ui.txtLevel3.text()
self.headings[3] = customizeHeadingsDlg.ui.txtLevel4.text()
self.headings[4] = customizeHeadingsDlg.ui.txtLevel5.text()
self.headings[5] = customizeHeadingsDlg.ui.txtLevel6.text()
self.headings[6] = customizeHeadingsDlg.ui.txtLevel7.text()
self.headings[7] = customizeHeadingsDlg.ui.txtLevel8.text()
def createProfile(self):
splitCh = '\t'
# 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
self.preferences['Last directory'] = stampFilename[0:stampFilename.lastIndexOf('/')]
# set profile specific parsing information
hierarchyStartIndex = self.startIndex
dataIndex = self.header.index('abundance')
# determine samples in profile
sampleNames = []
for i in xrange(1, len(self.data)):
sampleId = self.data[i].split(splitCh)[0]
if sampleId not in sampleNames:
sampleNames.append(sampleId)
# add profile info
profileDict = {}
parentMap = {}
for i in xrange(1, dataIndex-hierarchyStartIndex):
parentMap[i] = {}
for i in xrange(1, len(self.data)):
if self.data[i] == "":
continue # skip blank lines
lineSplit = self.data[i].split(splitCh)
if len(lineSplit) <= dataIndex:
QtGui.QMessageBox.information(self, 'Unrecognized file format', 'Your file does not appear to be a valid MG-RAST profile.')
return
count = int(lineSplit[dataIndex])
hierarchy = lineSplit[hierarchyStartIndex:dataIndex]
# replace '-' categories with parent
for i in xrange(1, len(hierarchy)):
if hierarchy[i] == '-':
if self.header[1] == 'domain':
hierarchy[i] = 'Unclassified ' + hierarchy[i-1]
else:
hierarchy[i] = hierarchy[i-1]
# force MG-RAST profile to be strictly tree-like
for i in xrange(1, len(hierarchy)):
parent = '-'.join(hierarchy[0:i])
child = hierarchy[i]
currentParentMap = parentMap[i]
parentList = currentParentMap.get(child, [])
if parent not in parentList:
parentList.append(parent)
parentMap[i][child] = parentList
parentIndex = parentList.index(parent)
if parentIndex != 0:
newChild = child + ' - #' + str(parentIndex)
hierarchy[i] = newChild
# add to profile
sampleId = lineSplit[0]
profileIndex = sampleNames.index(sampleId)
row = profileDict.get(hierarchy[-1], None)
if row == None:
row = ProfileRow()
row.countData = [0] * len(sampleNames)
row.hierarchy = hierarchy
profileDict[hierarchy[-1]] = row
row.countData[profileIndex] += count
# 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
fout.write(self.headings[0])
for heading in self.headings[1:(dataIndex-hierarchyStartIndex)]:
fout.write('\t' + heading)
for sampleName in sampleNames:
fout.write('\t' + sampleName)
fout.write('\n')
for key in profileDict.keys():
row = profileDict[key]
for h in row.hierarchy:
fout.write(h + '\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)