def __init__(self,expdat):
super(CorrelationWindow, self).__init__()
uic.loadUi(hs.get_data_path('correlation.py','ui'), self)
self.cexp=expdat
self.cField.addItems(expdat.fields)
self.bFieldValues1.clicked.connect(self.fieldvalues1)
self.tNewName.setText(self.cexp.studyname+'_de')
def __init__(self):
super(LoadWindow, self).__init__()
uic.loadUi(hs.get_data_path('load.py','ui'), self)
self.bLoadBrowseTable.clicked.connect(self.browsetable)
self.bLoadBrowseMap.clicked.connect(self.browsemap)
self.bLoadLoad.clicked.connect(self.load)
self.bLoadCancel.clicked.connect(self.cancel)
def __init__(self,expdat):
super(FilterSimilarSamplesWindow, self).__init__()
uic.loadUi(hs.get_data_path('filtersimilarsamples.py','ui'), self)
self.cexp=expdat
self.cField.addItems(expdat.fields)
self.bFieldValues1.clicked.connect(self.fieldvalues1)
self.tNewName.setText(self.cexp.studyname+'_fss')
def __init__(self,expdat):
super(PlotGUIWindow, self).__init__()
hs.Debug(1,hs.get_data_path('plotguiwindow.py','ui'))
uic.loadUi(os.path.join(hs.heatsequerdir,'ui/plotguiwindow.py'), self)
self.bGetSequence.clicked.connect(self.getsequence)
self.bExport.clicked.connect(self.export)
self.bView.clicked.connect(self.view)
self.bSave.clicked.connect(self.save)
self.bDBSave.clicked.connect(self.dbsave)
self.bEnrich.clicked.connect(self.enrich)
self.bExpInfo.clicked.connect(self.expinfo)
self.bSampleInfo.clicked.connect(self.sampleinfo)
self.connect(self.cSampleField, QtCore.SIGNAL('activated(QString)'), self.samplefield)
self.FigureTab.connect(self.FigureTab, QtCore.SIGNAL("currentChanged(int)"),self.tabchange)
self.cSampleField.setCurrentIndex(0)
self.cexp=expdat
self.selectionlines={}
self.selection=[]
self.setWindowTitle(self.cexp.studyname)
for cfield in self.cexp.fields:
self.cSampleField.addItem(cfield)
self.cPlotXField.addItem(cfield)
if self.cexp.seqdb:
ontofields,ontonames=hs.bactdb.getontonames(self.cexp.seqdb)
for conto in ontofields:
# for conto in self.cexp.seqdb.OntoGraph.keys():
self.cOntology.addItem(conto)
self.dc=None
self.createaddplot(useqt=True)
def __init__(self,expdat,cdb=False,bdb=False):
super(BiClusterWindow, self).__init__()
uic.loadUi(hs.get_data_path('bicluster.py','ui'), self)
self.cexp=expdat
self.cooldb=cdb
self.bactdb=bdb
self.lStudy.setText(self.cexp.studyname)
self.bBiCluster.clicked.connect(self.bicluster)
self.bView.clicked.connect(self.view)
def __init__(self,expdat):
super(FilterSamplesWindow, self).__init__()
uic.loadUi(hs.get_data_path('filtersamples.py','ui'), self)
self.cexp=expdat
self.cField.addItems(expdat.fields)
self.bOK.clicked.connect(self.OK)
self.bFieldValues.clicked.connect(self.fieldvalues)
self.cOverwrite.stateChanged.connect(self.overwrite)
self.bCancel.clicked.connect(self.cancel)
self.tNewName.setText(self.cexp.studyname+'_f')
def __init__(self, expdat):
super(DiffExpWindow, self).__init__()
uic.loadUi(hs.get_data_path("diffexp.py", "ui"), self)
self.cexp = expdat
self.cField.addItems(expdat.fields)
self.bFieldValues1.clicked.connect(self.fieldvalues1)
self.bFieldValues2.clicked.connect(self.fieldvalues2)
self.cAll.stateChanged.connect(self.allvalues)
# self.cField.stateChanged.connect(self.fieldchanged)
self.tNewName.setText(self.cexp.studyname + "_de")
def __init__(self,expdat):
super(ClassifyWindow, self).__init__()
uic.loadUi(hs.get_data_path('classifier.py','ui'), self)
self.cexp=expdat
self.cField.addItems(expdat.fields)
self.bFieldValues1.clicked.connect(self.fieldvalues1)
self.bFieldValues2.clicked.connect(self.fieldvalues2)
self.cAll.stateChanged.connect(self.allvalues)
# self.cField.stateChanged.connect(self.fieldchanged)
self.tNewName.setText(self.cexp.studyname+'_de')
def __init__(self,expdat):
super(AdvPlotWindow, self).__init__()
uic.loadUi(hs.get_data_path('advplot.py','ui'), self)
self.cexp=expdat
self.cField.addItems(expdat.fields)
self.bOK.clicked.connect(self.OK)
self.bFieldValues.clicked.connect(self.fieldvalues)
self.bMetaData.clicked.connect(self.metadata)
self.cSort.stateChanged.connect(self.usesort)
self.bCancel.clicked.connect(self.cancel)
def __init__(self,listdata=[],listname=''):
"""
create a list window with items in the list and the listname as specified
input:
listdata - the data to show in the list (a list)
listname - name to display above the list
"""
super(ListWindow, self).__init__()
uic.loadUi(hs.get_data_path('listwindow.py','ui'), self)
for citem in listdata:
self.lList.addItem(citem)
if listname:
self.lLabel.setText(listname)
def __init__(self,expdat):
super(MetaDataWindow, self).__init__()
uic.loadUi(hs.get_data_path('plotmetadata.py','ui'), self)
self.cexp=expdat
self.mddict={}
for cmeta in expdat.plotmetadata:
cname="%s;%s;%s;%s;%s" % (cmeta[0],cmeta[1],cmeta[2],cmeta[3],cmeta[4])
self.lMetaData.addItem(cname)
self.mddict[cname]=cmeta
self.bAdd.clicked.connect(self.add)
# the main list right mouse menu
self.lMetaData.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.lMetaData.connect(self.lMetaData, QtCore.SIGNAL("customContextMenuRequested(QPoint)"),self.listItemRightClicked)
def __init__(self,expdat):
super(PlotGUIWindow, self).__init__()
uic.loadUi(hs.get_data_path('plotguiwindow.py','ui'), self)
# uic.loadUi('ui/plotguiwindow.py', self)
self.bGetSequence.clicked.connect(self.getsequence)
self.bExport.clicked.connect(self.export)
self.bView.clicked.connect(self.view)
self.bSave.clicked.connect(self.save)
self.bDBSave.clicked.connect(self.dbsave)
self.bEnrich.clicked.connect(self.enrich)
self.bSampleInfo.clicked.connect(self.sampleinfo)
self.connect(self.cSampleField, QtCore.SIGNAL('activated(QString)'), self.samplefield)
self.FigureTab.connect(self.FigureTab, QtCore.SIGNAL("currentChanged(int)"),self.tabchange)
self.cSampleField.setCurrentIndex(0)
self.cexp=expdat
self.selectionlines={}
self.selection=[]
self.setWindowTitle(self.cexp.studyname)
for cfield in self.cexp.fields:
self.cSampleField.addItem(cfield)
self.cPlotXField.addItem(cfield)
if self.cexp.seqdb:
ontofields,ontonames=hs.bactdb.getontonames(self.cexp.seqdb)
for conto in ontofields:
# for conto in self.cexp.seqdb.OntoGraph.keys():
self.cOntology.addItem(conto)
# add the matplotlib figure
self.frame = QtGui.QWidget(self)
self.dc = MyMplCanvas(self.frame, width=5, height=4, dpi=100)
# add it to an hboxlayout to make it resize with window
layout = QtGui.QHBoxLayout(self)
layout.insertSpacing(0,250)
# layout.addWidget(self.dc)
# self.setLayout(layout)
layout2 = QtGui.QVBoxLayout()
layout.addLayout(layout2)
layout2.addWidget(self.dc)
self.mpl_toolbar = NavigationToolbar(self.dc, self)
layout2.addWidget(self.mpl_toolbar)
self.setLayout(layout)
def __init__(self,expdat):
super(PlotGUIWindow, self).__init__()
hs.Debug(1,hs.get_data_path('plotguiwindow.py','ui'))
uic.loadUi(os.path.join(hs.heatsequerdir,'ui/plotguiwindow.py'), self)
self.bGetSequence.clicked.connect(self.getsequence)
self.bExport.clicked.connect(self.export)
self.bView.clicked.connect(self.view)
self.bSave.clicked.connect(self.save)
self.bDBSave.clicked.connect(self.dbsave)
self.bEnrich.clicked.connect(self.enrich)
self.bExpInfo.clicked.connect(self.expinfo)
self.bSampleInfo.clicked.connect(self.sampleinfo)
self.lCoolDB.doubleClicked.connect(self.showannotation)
self.cSampleField.activated.connect(self.samplefield)
self.FigureTab.currentChanged.connect(self.tabchange)
self.cSampleField.setCurrentIndex(0)
self.cexp=expdat
self.selectionlines={}
self.selection=[]
self.setWindowTitle(self.cexp.studyname)
for cfield in self.cexp.fields:
self.cSampleField.addItem(cfield)
self.cPlotXField.addItem(cfield)
if self.cexp.seqdb:
ontofields,ontonames=hs.bactdb.getontonames(self.cexp.seqdb)
for conto in ontofields:
# for conto in self.cexp.seqdb.OntoGraph.keys():
self.cOntology.addItem(conto)
self.dc=None
self.createaddplot(useqt=True)
# right click menu
self.lCoolDB.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.lCoolDB.customContextMenuRequested.connect(self.listItemRightClicked)
def __init__(self,expdat):
super(JoinWindow, self).__init__()
uic.loadUi(hs.get_data_path('joinfields.py','ui'), self)
self.cexp=expdat
self.cField1.addItems(expdat.fields)
self.cField2.addItems(expdat.fields)
def __init__(self,expdat):
super(MetaDataDetailsWindow, self).__init__()
uic.loadUi(hs.get_data_path('metadatadetails.py','ui'), self)
self.cexp=expdat
self.bFieldValues.clicked.connect(self.values)
self.cField.addItems(expdat.fields)
def __init__(self):
super(AppWindow, self).__init__()
uic.loadUi(hs.get_data_path('appwindow.py','ui'), self)
self.bMainLoadNew.clicked.connect(self.load)
self.bPickleLoad.clicked.connect(self.pickleload)
self.bMainPlot.clicked.connect(self.plot)
self.bMainAdvancedPlot.clicked.connect(self.advplot)
self.bMainFilterSamples.clicked.connect(self.filtersamples)
self.bDiffExp.clicked.connect(self.diffexp)
self.bCorrelation.clicked.connect(self.correlation)
self.bFilterSimilarSamples.clicked.connect(self.filtersimilarsamples)
self.bClassifier.clicked.connect(self.classify)
self.bFilterOrigReads.clicked.connect(self.filterorigreads)
self.bMainSortSamples.clicked.connect(self.sortsamples)
self.bMainClusterBacteria.clicked.connect(self.clusterbacteria)
self.bMainFilterMinReads.clicked.connect(self.filterminreads)
self.bMainFilterTaxonomy.clicked.connect(self.filtertaxonomy)
self.bFilterAnnotation.clicked.connect(self.filterannotation)
self.bFilterPresence.clicked.connect(self.filterpresence)
self.bFilterMean.clicked.connect(self.filtermean)
self.bSortAbundance.clicked.connect(self.sortabundance)
self.bJoinFields.clicked.connect(self.joinfields)
self.bJoinExps.clicked.connect(self.joinexps)
self.bBicluster.clicked.connect(self.bicluster)
self.bEnrichment.clicked.connect(self.enrichment)
self.bFilterFasta.clicked.connect(self.filterfasta)
self.bRenormalize.clicked.connect(self.renormalize)
self.bCleanTaxonomy.clicked.connect(self.cleantaxonomy)
self.bSubsample.clicked.connect(self.subsample)
self.cDebugMode.stateChanged.connect(self.debugmode)
# the main list right mouse menu
self.bMainList.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.bMainList.connect(self.bMainList, QtCore.SIGNAL("customContextMenuRequested(QPoint)"),self.listItemRightClicked)
self.show()
self.bactdb=False
self.cooldb=False
try:
hs.Debug(6,'Connecting to sequence database')
bdbpath=hs.get_data_path('SRBactDB.db','db')
hs.Debug(6,'From %s' % bdbpath)
self.bactdb=hs.bactdb.dbstart(bdbpath)
hs.Debug(6,'Sequence database connected')
except:
hs.Debug(9,'sequence database file not found')
try:
hs.Debug(6,'Loading coolseq database')
cdbpath=hs.get_data_path('coolseqs.txt','db')
hs.Debug(6,'From %s' % cdbpath)
self.cooldb=hs.cooldb.loaddb(cdbpath)
hs.Debug(6,'coolseq database loaded')
except:
hs.Debug(9,'CoolDB file not found')
# put some experiments:
hs.Debug(6,'Loading sample experiment')
try:
expdat=hs.load('./test_data/bears.clean.new.withtax.biom','./test_data/map.txt')
self.addexp(expdat)
except:
hs.Debug(6,'Sample experiment not found. sorry')
def __init__(self,expdat):
super(CleanTaxonomyWindow, self).__init__()
uic.loadUi(hs.get_data_path('cleantaxonomy.py','ui'), self)
self.cexp=expdat
def __init__(self):
super(FilterFastaWindow, self).__init__()
uic.loadUi(hs.get_data_path('filterfasta.py','ui'), self)
self.bBrowse.clicked.connect(self.browse)
