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
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
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')