def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileBiomDlg()
self.ui.setupUi(self)
self.preferences = preferences
self.centerWindow()
QtCore.QObject.connect(self.ui.btnBiomFile, QtCore.SIGNAL("clicked()"),
self.loadBiomFile)
QtCore.QObject.connect(self.ui.btnCreateProfile,
QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"),
self.accept)
self.biomFile = None
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileBiomDlg()
self.ui.setupUi(self)
self.preferences = preferences
self.centerWindow()
QtCore.QObject.connect(self.ui.btnBiomFile, QtCore.SIGNAL("clicked()"), self.loadBiomFile)
QtCore.QObject.connect(self.ui.btnCreateProfile, QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"), self.accept)
self.biomFile = None
class CreateProfileBiomDlg(QtGui.QDialog):
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileBiomDlg()
self.ui.setupUi(self)
self.preferences = preferences
self.centerWindow()
QtCore.QObject.connect(self.ui.btnBiomFile, QtCore.SIGNAL("clicked()"), self.loadBiomFile)
QtCore.QObject.connect(self.ui.btnCreateProfile, QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"), self.accept)
self.biomFile = None
def loadBiomFile(self):
selectedFile = QtGui.QFileDialog.getOpenFileName(self, 'Load BIOM file', self.preferences['Last directory'], 'BIOM file (*.biom);;Compressed BIOM file (*.gz);;All files (*.*)')
if selectedFile != '':
self.preferences['Last directory'] = selectedFile[0:selectedFile.lastIndexOf('/')]
self.ui.txtBiomFile.setText(selectedFile)
self.biomFile = selectedFile
def createProfile(self):
# determine group for each sequence ID
if self.biomFile == None:
QtGui.QMessageBox.information(self, 'Missing data', 'A BIOM file must be specified.', QtGui.QMessageBox.Ok)
return
outputFile = QtGui.QFileDialog.getSaveFileName(self, 'Save STAMP profile...', self.preferences['Last directory'],'STAMP profile file(*.spf);;All files(*.*)')
if outputFile == '':
return
self.convertBiomFileToStampProfile(str(self.biomFile), str(outputFile), str(self.ui.cboMetadataField.currentText()))
self.accept()
def centerWindow(self):
screen = QtGui.QDesktopWidget().screenGeometry()
size = self.geometry()
self.move((screen.width()-size.width())/2, (screen.height()-size.height())/2)
def convertBiomFileToStampProfile(self, file_name, output_name, metadata_name):
""" Function taken from PICRUSt by Morgan Langill.
https://github.com/mlangill/get_mgrast_data/blob/master/biom_to_stamp.py
"""
#allow file to be optionally gzipped (must use extension '.gz')
ext=splitext(file_name)[1]
if (ext == '.gz'):
table = parse_biom_table(gzip.open(file_name,'rb'))
else:
table = parse_biom_table(open(file_name,'U'))
metadata_name = metadata_name.split('(')[0].rstrip()
if metadata_name is None or metadata_name == '<observation ids>':
max_len_metadata = 0
elif table.ObservationMetadata and metadata_name in table.ObservationMetadata[0]:
#figure out the longest list within the given metadata
max_len_metadata = max(len(p[metadata_name]) for p in table.ObservationMetadata)
else:
QtGui.QMessageBox.information(self, 'Unrecognized metadata file', "'" + metadata_name + "' was not found in the BIOM table.", QtGui.QMessageBox.Ok)
return
#make the header line
header=[]
#make simple labels for each level in the metadata (e.g. 'Level_1', 'Level_2', etc.) "+1" for the observation id as well.
for i in range(max_len_metadata):
header.append('Level_'+ str(i+1))
header.append('Observation Ids')
#add the sample ids to the header line
header.extend(table.SampleIds)
fout = open(output_name, 'w')
fout.write("\t".join(header) + '\n')
#now process each observation (row in the table)
for obs_vals, obs_id, obs_metadata in table.iterObservations():
row=[]
if max_len_metadata > 0:
row = obs_metadata[metadata_name]
# add blanks if the metadata doesn't fill each level
if len(row) < max_len_metadata:
for i in range(max_len_metadata - len(row)):
row.append('unclassified')
#Add the observation id as the last "Level"
row.append(obs_id)
#Add count data to the row
row.extend(map(str,obs_vals))
fout.write("\t".join(row) + '\n')
fout.close()
class CreateProfileBiomDlg(QtGui.QDialog):
def __init__(self, preferences, parent=None):
QtGui.QWidget.__init__(self, parent)
# initialize GUI
self.ui = Ui_CreateProfileBiomDlg()
self.ui.setupUi(self)
self.preferences = preferences
self.centerWindow()
QtCore.QObject.connect(self.ui.btnBiomFile, QtCore.SIGNAL("clicked()"),
self.loadBiomFile)
QtCore.QObject.connect(self.ui.btnCreateProfile,
QtCore.SIGNAL("clicked()"), self.createProfile)
QtCore.QObject.connect(self.ui.btnCancel, QtCore.SIGNAL("clicked()"),
self.accept)
self.biomFile = None
def loadBiomFile(self):
selectedFile = QtGui.QFileDialog.getOpenFileName(
self, 'Load BIOM file', self.preferences['Last directory'],
'BIOM file (*.biom);;Compressed BIOM file (*.gz);;All files (*.*)')
if selectedFile != '':
self.preferences['Last directory'] = selectedFile[0:selectedFile.
lastIndexOf('/')]
self.ui.txtBiomFile.setText(selectedFile)
self.biomFile = selectedFile
def createProfile(self):
# determine group for each sequence ID
if self.biomFile == None:
QtGui.QMessageBox.information(self, 'Missing data',
'A BIOM file must be specified.',
QtGui.QMessageBox.Ok)
return
outputFile = QtGui.QFileDialog.getSaveFileName(
self, 'Save STAMP profile...', self.preferences['Last directory'],
'STAMP profile file(*.spf);;All files(*.*)')
if outputFile == '':
return
self.convertBiomFileToStampProfile(
str(self.biomFile), str(outputFile),
str(self.ui.cboMetadataField.currentText()))
self.accept()
def centerWindow(self):
screen = QtGui.QDesktopWidget().screenGeometry()
size = self.geometry()
self.move((screen.width() - size.width()) / 2,
(screen.height() - size.height()) / 2)
def convertBiomFileToStampProfile(self, file_name, output_name,
metadata_name):
""" Function taken from PICRUSt by Morgan Langill.
https://github.com/mlangill/get_mgrast_data/blob/master/biom_to_stamp.py
"""
#allow file to be optionally gzipped (must use extension '.gz')
ext = splitext(file_name)[1]
if (ext == '.gz'):
table = parse_biom_table(gzip.open(file_name, 'rb'))
else:
table = parse_biom_table(open(file_name, 'U'))
metadata_name = metadata_name.split('(')[0].rstrip()
if metadata_name is None or metadata_name == '<observation ids>':
max_len_metadata = 0
elif table.observation_metadata and metadata_name in table.observation_metadata[
0]:
#figure out the longest list within the given metadata
max_len_metadata = max(
len(p[metadata_name]) for p in table.observation_metadata)
else:
QtGui.QMessageBox.information(
self, 'Unrecognized metadata file',
"'" + metadata_name + "' was not found in the BIOM table.",
QtGui.QMessageBox.Ok)
return
#make the header line
header = []
#make simple labels for each level in the metadata (e.g. 'Level_1', 'Level_2', etc.) "+1" for the observation id as well.
for i in range(max_len_metadata):
header.append('Level_' + str(i + 1))
header.append('Observation Ids')
#add the sample ids to the header line
header.extend(table.sample_ids)
fout = open(output_name, 'w')
fout.write("\t".join(header) + '\n')
#now process each observation (row in the table)
for obs_vals, obs_id, obs_metadata in table.iter(axis='observation'):
row = []
if max_len_metadata > 0:
row = obs_metadata[metadata_name]
# add blanks if the metadata doesn't fill each level
if len(row) < max_len_metadata:
for i in range(max_len_metadata - len(row)):
row.append('unclassified')
#Add the observation id as the last "Level"
if isNumber(obs_id):
row.append('ID' + obs_id)
else:
row.append(obs_id)
#Add count data to the row
row.extend(map(str, obs_vals))
fout.write("\t".join(row) + '\n')
fout.close()
