Esempio n. 1
0
	def load(self):
		loadwin = LoadWindow()
		res=loadwin.exec_()
		if res==QtGui.QDialog.Accepted:
			tablefname=str(loadwin.tLoadTable.text())
			mapfname=str(loadwin.tLoadMap.text())
			expname=str(loadwin.tLoadName.text())
			metabolite=loadwin.cMetabolite.checkState()
			if metabolite:
				tabletype='meta'
			else:
				tabletype='biom'
			expdat=hs.load(tablefname,mapfname,tabletype=tabletype)
			expdat.studyname=expname
			self.addexp(expdat)
			# for biom table show the number of reads`
			if tabletype=='biom':
#				hs.analyzenumreads(expdat)
				pass
Esempio n. 2
0
 def load(self):
     loadwin = LoadWindow()
     res = loadwin.exec_()
     if res == QtWidgets.QDialog.Accepted:
         tablefname = str(loadwin.tLoadTable.text())
         mapfname = str(loadwin.tLoadMap.text())
         expname = str(loadwin.tLoadName.text())
         metabolite = loadwin.cMetabolite.checkState()
         emp = loadwin.cEMP.checkState()
         normalize = not loadwin.cNoNormalize.checkState()
         if metabolite:
             tabletype = "meta"
         else:
             tabletype = "biom"
         expdat = hs.load(tablefname, mapfname, tabletype=tabletype, mapsampletolowercase=emp, normalize=normalize)
         expdat.studyname = expname
         self.addexp(expdat)
         # for biom table show the number of reads`
         if tabletype == "biom":
             # 				hs.analyzenumreads(expdat)
             pass
Esempio n. 3
0
	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')