/
hsgui.py
executable file
·1212 lines (1032 loc) · 37.5 KB
/
hsgui.py
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#!/usr/bin/env python
"""
heatsequer full gui
"""
# amnonscript
__version__ = "0.91"
import heatsequer as hs
import sys
from PyQt5 import QtGui, uic, QtCore, QtWidgets
# import cPickle as pickle
#import cPickle as pickle
import pickle
import matplotlib
matplotlib.use('Qt5Agg')
import os.path
import numpy as np
class CleanTaxonomyWindow(QtWidgets.QDialog):
cexp=[]
def __init__(self,expdat):
super(CleanTaxonomyWindow, self).__init__()
uic.loadUi(hs.get_data_path('cleantaxonomy.py','ui'), self)
self.cexp=expdat
class JoinWindow(QtWidgets.QDialog):
cexp=[]
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)
class MetaDataDetailsWindow(QtWidgets.QDialog):
cexp=[]
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 values(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
if ok:
self.tValue.setText(val)
class MetaDataWindow(QtWidgets.QDialog):
cexp=[]
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 listItemRightClicked(self, QPos):
self.listMenu= QtWidgets.QMenu()
menuremove = self.listMenu.addAction("Remove Item")
self.connect(menuremove, QtCore.SIGNAL("triggered()"), self.menuRemove)
parentPosition = self.lMetaData.mapToGlobal(QtCore.QPoint(0, 0))
self.listMenu.move(parentPosition + QPos)
self.listMenu.show()
def menuRemove(self):
if len(self.lMetaData.selectedItems())>1:
if QtWidgets.QMessageBox.warning(self,"Remove metadata?","Remove %d limes?" % len(self.lMetaData.selectedItems()),QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)==QtWidgets.QMessageBox.No:
return
for currentItemName in self.lMetaData.selectedItems():
currentItemName=str(currentItemName.text())
# currentItemName=str(self.bMainList.currentItem().text())
self.removemetadata(currentItemName)
def removemetadata(self,mdname):
del self.mddict[mdname]
items=self.lMetaData.findItems(mdname,QtCore.Qt.MatchExactly)
for item in items:
self.lMetaData.takeItem(self.lMetaData.row(item))
def add(self):
metadatadetailswin = MetaDataDetailsWindow(self.cexp)
res=metadatadetailswin.exec_()
if res==QtWidgets.QDialog.Accepted:
cmeta=[]
cmeta.append(str(metadatadetailswin.cField.currentText()))
cmeta.append(str(metadatadetailswin.tValue.text()))
cmeta.append(str(metadatadetailswin.tColor.text()))
cmeta.append(metadatadetailswin.cInverse.checkState())
cmeta.append(metadatadetailswin.cBefore.checkState())
cname="%s;%s;%s;%s;%s" % (cmeta[0],cmeta[1],cmeta[2],cmeta[3],cmeta[4])
self.lMetaData.addItem(cname)
self.mddict[cname]=cmeta
class BiClusterWindow(QtWidgets.QDialog):
cexp=[]
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 bicluster(self):
newexp,seqs,samples=hs.bicluster(self.cexp,method='binary',sampkeep=0,bactkeep=0,justcount=True)
self.samples=samples[0]
self.seqs=seqs[0]
self.lNumSamples.setText(str(len(self.samples)))
self.lNumBacteria.setText(str(len(self.seqs)))
self.lSamples.clear()
self.lBacteria.clear()
# get the new bacteria and sample order
allsamp=np.arange(len(self.cexp.samples))
allbact=np.arange(len(self.cexp.seqs))
x=np.setdiff1d(allsamp,self.samples)
sampo=np.concatenate((self.samples,x))
ubact=[]
for cseq in self.seqs:
ubact.append(self.cexp.seqdict[cseq])
bacto=np.concatenate((ubact,np.setdiff1d(allbact,ubact)))
self.cexp.bactorder=bacto
self.cexp.samporder=sampo
# if we have enough bacteria and samples, update the info list
if len(self.seqs)>=5 and len(self.samples)>=5:
sampmd=hs.testmdenrichmentall(self.cexp,self.samples)
for cmd in sampmd:
if cmd['observed']<cmd['expected']:
ccolor=QtGui.QColor(155,0,0)
else:
ccolor=QtGui.QColor(0,155,0)
item = QtWidgets.QListWidgetItem()
item.setText("%s - %s (p:%f o:%d e:%f)" % (cmd['field'],cmd['val'],cmd['pval'],cmd['observed'],cmd['expected']))
item.setForeground(ccolor)
self.lSamples.addItem(item)
if self.cooldb:
bmd=hs.annotationenrichment(self.cexp,self.seqs)
# bmd=hs.cooldb.testenrichment(self.cooldb,self.cexp.seqs,self.seqs)
bmd=hs.sortenrichment(bmd)
for cbmd in bmd:
if cbmd['observed']<cbmd['expected']:
ccolor=QtGui.QColor(155,0,0)
else:
ccolor=QtGui.QColor(0,155,0)
item = QtWidgets.QListWidgetItem()
item.setText("%s (p:%f o:%d e:%f)" % (cbmd['description'],cbmd['pval'],cbmd['observed'],cbmd['expected']))
item.setForeground(ccolor)
self.lBacteria.addItem(item)
# self.lBacteria.addItem("%s (p:%f o:%d e:%f)" % (cbmd['description'],cbmd['pval'],cbmd['observed'],cbmd['expected']))
def view(self):
cexp=self.cexp
allsamp=np.arange(len(cexp.samples))
allbact=np.arange(len(cexp.seqs))
x=np.setdiff1d(allsamp,self.samples)
sampo=np.concatenate((self.samples,x))
ubact=[]
for cseq in self.seqs:
ubact.append(cexp.seqdict[cseq])
bacto=np.concatenate((ubact,np.setdiff1d(allbact,ubact)))
newexp=hs.reorderbacteria(cexp,bacto)
newexp=hs.reordersamples(newexp,sampo,inplace=True)
hs.plotexp(newexp,seqdb=self.bactdb,sortby=False,numeric=False,usegui=True,cdb=self.cooldb,showline=False)
class AdvPlotWindow(QtWidgets.QDialog):
cexp=[]
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 metadata(self):
metadatawin = MetaDataWindow(self.cexp)
res=metadatawin.exec_()
if res==QtWidgets.QDialog.Accepted:
self.cexp.plotmetadata=metadatawin.mddict.values()
def cancel(self):
self.reject()
def OK(self):
self.accept()
def fieldvalues(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
def usesort(self):
# unchecked
if self.cSort.checkState()==0:
self.cField.setEnabled(False)
else:
self.cField.setEnabled(True)
class SortSamplesWindow(QtWidgets.QDialog):
cexp=[]
def __init__(self,expdat):
super(SortSamplesWindow, self).__init__()
uic.loadUi(hs.get_data_path('sortsamples.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+'_s')
def cancel(self):
self.reject()
def OK(self):
self.accept()
def fieldvalues(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
def overwrite(self):
# unchecked
if self.cOverwrite.checkState()==0:
self.tNewName.setText(self.cexp.studyname+'_s')
self.tNewName.setReadOnly(False)
else:
self.tNewName.setText(self.cexp.studyname)
self.tNewName.setReadOnly(True)
class DiffExpWindow(QtWidgets.QDialog):
cexp=[]
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 fieldchanged(self):
# self.tNewName.setText(self.cexp.studyname+'_'+str(self.cField.currentText())+'_de')
def fieldvalues1(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
if ok:
self.tValue1.setText(val)
def fieldvalues2(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
if ok:
self.tValue2.setText(val)
def allvalues(self):
# unchecked
if self.cAll.checkState()==0:
self.tValue2.setReadOnly(False)
else:
self.tValue2.setReadOnly(True)
class FilterSimilarSamplesWindow(QtWidgets.QDialog):
cexp=[]
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 fieldvalues1(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
class CorrelationWindow(QtWidgets.QDialog):
cexp=[]
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 fieldvalues1(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
class ClassifyWindow(QtWidgets.QDialog):
cexp=[]
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 fieldchanged(self):
# self.tNewName.setText(self.cexp.studyname+'_'+str(self.cField.currentText())+'_de')
def fieldvalues1(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
if ok:
self.tValue1.setText(val)
def fieldvalues2(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
if ok:
self.tValue2.setText(val)
def allvalues(self):
# unchecked
if self.cAll.checkState()==0:
self.tValue2.setReadOnly(False)
else:
self.tValue2.setReadOnly(True)
class FilterSamplesWindow(QtWidgets.QDialog):
cexp=[]
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 cancel(self):
self.reject()
def OK(self):
self.accept()
def fieldvalues(self):
cfield=str(self.cField.currentText())
val,ok=QtWidgets.QInputDialog.getItem(self,'Select field value','Field=%s' % cfield,list(set(hs.getfieldvals(self.cexp,cfield))))
if ok:
self.tValue.setText(val)
def overwrite(self):
# unchecked
if self.cOverwrite.checkState()==0:
self.tNewName.setText(self.cexp.studyname+'_f')
self.tNewName.setReadOnly(False)
else:
self.tNewName.setText(self.cexp.studyname)
self.tNewName.setReadOnly(True)
class FilterFastaWindow(QtWidgets.QDialog):
def __init__(self):
super(FilterFastaWindow, self).__init__()
uic.loadUi(hs.get_data_path('filterfasta.py','ui'), self)
self.bBrowse.clicked.connect(self.browse)
def browse(self):
fname,_ = QtWidgets.QFileDialog.getOpenFileName(self, 'Open fasta file',filter='*.fa;;*.fasta;;*.fna')
fname=str(fname)
self.tFileName.setText(fname)
class LoadWindow(QtWidgets.QDialog):
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 browsemap(self):
fname,_ = QtWidgets.QFileDialog.getOpenFileName(self, 'Open map file',filter='*.txt')
fname=str(fname)
self.tLoadMap.setText(fname)
def browsetable(self):
fname,_ = QtWidgets.QFileDialog.getOpenFileName(self, 'Open table file','')
fname=str(fname)
self.tLoadTable.setText(fname)
pname=os.path.basename(fname)
self.tLoadName.setText(pname)
def load(self):
self.accept()
def cancel(self):
self.reject()
class ListWindow(QtWidgets.QDialog):
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)
class AppWindow(QtWidgets.QMainWindow):
# the experiments loaded for analysis
explist={}
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.customContextMenuRequested.connect(self.listItemRightClicked)
# 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 listItemRightClicked(self, QPos):
self.listMenu= QtWidgets.QMenu()
menurename = self.listMenu.addAction("Rename")
menurename.triggered.connect(self.menuRename)
menuremove = self.listMenu.addAction("Delete")
menuremove.triggered.connect(self.menuRemove)
menusave = self.listMenu.addAction("Save (pickle) Item")
menusave.triggered.connect(self.menuSave)
menuexport = self.listMenu.addAction("Save (biom) Item")
menuexport.triggered.connect(self.menuExport)
menuexportnorenorm = self.listMenu.addAction("Save (biom relative abund) Item")
menuexportnorenorm.triggered.connect(self.menuExportNoRenorm)
menuinfo = self.listMenu.addAction("Info")
menuinfo.triggered.connect(self.expinfo)
parentPosition = self.bMainList.mapToGlobal(QtCore.QPoint(0, 0))
menusavecommands = self.listMenu.addAction("Save commands")
menusavecommands.triggered.connect(self.menuSaveCommands)
self.listMenu.move(parentPosition + QPos)
self.listMenu.show()
def expinfo(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
listwin = ListWindow(cexp.filters,cexp.studyname)
res=listwin.exec_()
def menuRename(self):
if len(self.bMainList.selectedItems())>1:
return
for citem in self.bMainList.selectedItems():
cname=str(citem.text())
cexp=self.explist[cname]
val,ok=QtWidgets.QInputDialog.getText(self,'Rename experiment','old name=%s' % cname)
if ok:
self.removeexp(cname)
cexp.studyname=val
self.addexp(cexp)
def menuRemove(self):
if len(self.bMainList.selectedItems())>1:
if QtWidgets.QMessageBox.warning(self,"Remove samples?","Remove %d samples?" % len(self.bMainList.selectedItems()),QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)==QtWidgets.QMessageBox.No:
return
for currentItemName in self.bMainList.selectedItems():
currentItemName=str(currentItemName.text())
# currentItemName=str(self.bMainList.currentItem().text())
self.removeexp(currentItemName)
def menuSave(self):
cname=str(self.bMainList.currentItem().text())
fname,_ = QtWidgets.QFileDialog.getSaveFileName(self, 'Save experiment as pickle','')
fname=str(fname)
fl=open(fname,'w')
pickle.dump(self.explist[cname],fl,-1)
fl.close()
QtWidgets.QMessageBox.information(self,'Analysis','experiment %s saved as pickle' % cname)
# picklewrapper.save('test',currentItemName)
def menuExport(self):
cname=str(self.bMainList.currentItem().text())
fname,_ = QtWidgets.QFileDialog.getSaveFileName(self, 'Save experiment as biom','')
fname=str(fname)
hs.savetobiom(self.explist[cname],fname,'hdf5')
QtWidgets.QMessageBox.information(self,'Analysis','experiment %s saved as biom table and mapping file' % cname)
# cname=str(self.bMainList.currentItem().text())
# cm='global %s;%s=self.explist[cname]' % (cname,cname)
# exec(cm)
# hs.Debug(7,'exported',cname)
def menuExportNoRenorm(self):
cname=str(self.bMainList.currentItem().text())
fname,_ = QtWidgets.QFileDialog.getSaveFileName(self, 'Save experiment as biom','')
fname=str(fname)
hs.savetobiom(self.explist[cname],fname,'hdf5',useorigreads=False)
QtWidgets.QMessageBox.information(self,'Analysis','experiment %s saved as non-orig-reads biom table and mapping file' % cname)
def menuSaveCommands(self):
cname=str(self.bMainList.currentItem().text())
fname,_ = QtWidgets.QFileDialog.getSaveFileName(self, 'Save experiment python commands','.py')
fname=str(fname)
hs.savecommands(self.explist[cname],fname)
QtWidgets.QMessageBox.information(self,'Analysis','experiment %s commands saved to file:\n%s' % (cname,fname))
def addexp(self,expdat):
"""
add a new experiment to the list
"""
# make sure the experiment is not already in the list
# if so, give a new unique name
expname=expdat.studyname
cnum=1
while expname in self.explist:
expname=expdat.studyname+str(cnum)
cnum+=1
expdat.studyname=expname
expdname='%s (%s-S, %s-B)' % (expname,hs.nicenum(len(expdat.samples)),hs.nicenum(len(expdat.sids)))
self.explist[expdname]=expdat
self.bMainList.addItem(expdname)
self.bMainList.clearSelection()
self.bMainList.setCurrentRow(self.bMainList.count()-1)
expdat.seqdb=self.bactdb
expdat.cooldb=self.cooldb
def replaceexp(self,expdat):
"""
replace an existing experiment with new values
"""
expname=expdat.studyname
self.explist[expname]=expdat
items=self.bMainList.findItems(expname,QtCore.Qt.MatchExactly)
for item in items:
self.bMainList.takeItem(self.bMainList.row(item))
self.bMainList.addItem(expname)
def removeexp(self,expname):
"""
remove an experiment from the list (and clear)
"""
del self.explist[expname]
items=self.bMainList.findItems(expname,QtCore.Qt.MatchExactly)
for item in items:
self.bMainList.takeItem(self.bMainList.row(item))
def joinfields(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
joinwin = JoinWindow(cexp)
res=joinwin.exec_()
if res==QtWidgets.QDialog.Accepted:
fieldname1=str(joinwin.cField1.currentText())
fieldname2=str(joinwin.cField2.currentText())
newfieldname=str(joinwin.lineEdit.text())
expdat=hs.joinfields(cexp,fieldname1,fieldname2,newfieldname)
self.addexp(expdat)
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 pickleload(self):
fname,_ = QtWidgets.QFileDialog.getOpenFileName(self, 'Open pickle file')
fname=str(fname)
if fname:
fl=open(fname,'r')
expdat=pickle.load(fl)
if isinstance(expdat,hs.Experiment):
self.addexp(expdat)
else:
hs.Debug(9,'Not an experiment pickle!')
print(type(expdat))
def plot(self):
items=self.bMainList.selectedItems()
for citem in items:
cname=str(citem.text())
hs.plotexp(self.explist[cname],usegui=True,sortby=False,seqdb=self.bactdb,cdb=self.cooldb)
def advplot(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
dwin = AdvPlotWindow(cexp)
res=dwin.exec_()
if res==QtWidgets.QDialog.Accepted:
minreads=dwin.sMinReads.value()
cnumeric=dwin.cNumeric.checkState()
if cnumeric==0:
numeric=False
else:
numeric=True
cshowline=dwin.cLines.checkState()
if cshowline==0:
showline=False
else:
showline=True
csort=dwin.cSort.checkState()
if csort==0:
sortfield=False
else:
sortfield=str(dwin.cField.currentText())
cscalebar=dwin.cScaleBar.checkState()
if cscalebar==0:
showcolorbar=False
else:
showcolorbar=True
crangeall=dwin.cRangeAll.checkState()
if crangeall==0:
rangeall=False
else:
rangeall=True
hs.plotexp(cexp,sortby=sortfield,numeric=numeric,showline=showline,minreads=minreads,usegui=True,cdb=self.cooldb,seqdb=self.bactdb,rangeall=rangeall,showcolorbar=showcolorbar)
def filterfasta(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
filterfastawin = FilterFastaWindow()
res=filterfastawin.exec_()
if res==QtWidgets.QDialog.Accepted:
filename=str(filterfastawin.tFileName.text())
exclude=filterfastawin.cExclude.checkState()
pmatch=filterfastawin.cPartialMatch.checkState()
newname=str(filterfastawin.tNewName.text())
if not newname:
newname=cexp.studyname+'-ffa'
overwrite=filterfastawin.cOverwrite.checkState()
newexp=hs.filterfasta(cexp,filename,exclude=exclude,subseq=pmatch)
if overwrite==0:
newexp.studyname=newname
self.addexp(newexp)
else:
self.replaceexp(newexp)
def diffexp(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
diffexpwin = DiffExpWindow(cexp)
res=diffexpwin.exec_()
if res==QtWidgets.QDialog.Accepted:
field=str(diffexpwin.cField.currentText())
value1=str(diffexpwin.tValue1.text())
value2=str(diffexpwin.tValue2.text())
newname=str(diffexpwin.tNewName.text())
method=str(diffexpwin.cMethod.currentText())
fdr=diffexpwin.sFDR.value()
compareall=diffexpwin.cAll.checkState()
if compareall:
value2=False
if method=='all':
newexp=hs.getdiffsigall(cexp,field,value1,value2,maxfval=fdr)
else:
newexp=hs.getdiffsig(cexp,field,value1,value2,method=method,maxfval=fdr)
if newexp:
newexp.studyname=newname+'_'+field
self.addexp(newexp)
def filtersimilarsamples(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
filtersimsampwin = FilterSimilarSamplesWindow(cexp)
res=filtersimsampwin.exec_()
if res==QtWidgets.QDialog.Accepted:
field=str(filtersimsampwin.cField.currentText())
newname=str(filtersimsampwin.tNewName.text())
method=str(filtersimsampwin.cMethod.currentText())
newexp=hs.filtersimilarsamples(cexp,field=field,method=method)
if newexp:
newexp.studyname=newname
self.addexp(newexp)
def correlation(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
diffexpwin = CorrelationWindow(cexp)
res=diffexpwin.exec_()
if res==QtWidgets.QDialog.Accepted:
field=str(diffexpwin.cField.currentText())
newname=str(diffexpwin.tNewName.text())
method=str(diffexpwin.cMethod.currentText())
numeric=diffexpwin.cNumeric.checkState()
newexp=hs.getsigcorr(cexp,field,numeric=numeric,method=method)
if newexp:
newexp.studyname=newname+'_cor_'+field
self.addexp(newexp)
def classify(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
classifywin = ClassifyWindow(cexp)
res=classifywin.exec_()
if res==QtWidgets.QDialog.Accepted:
field=str(classifywin.cField.currentText())
value1=str(classifywin.tValue1.text())
value2=str(classifywin.tValue2.text())
method=str(classifywin.cMethod.currentText())
compareall=classifywin.cAll.checkState()
if compareall:
value2=False
auc=hs.BaysZeroClassifyTest(cexp,field,value1,value2,numiter=5)
hs.Debug(6,"AUC is %f" % auc)
def filtersamples(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
filtersampleswin = FilterSamplesWindow(cexp)
res=filtersampleswin.exec_()
if res==QtWidgets.QDialog.Accepted:
field=str(filtersampleswin.cField.currentText())
value=str(filtersampleswin.tValue.text())
newname=str(filtersampleswin.tNewName.text())
overwrite=filtersampleswin.cOverwrite.checkState()
exclude=filtersampleswin.cExclude.checkState()
exact=filtersampleswin.cExact.checkState()
newexp=hs.filtersamples(cexp,field,value,exclude=exclude,exact=exact)
if overwrite==0:
newexp.studyname=newname
self.addexp(newexp)
else:
self.replaceexp(newexp)
def sortabundance(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
filtersampleswin = FilterSamplesWindow(cexp)
res=filtersampleswin.exec_()
if res==QtWidgets.QDialog.Accepted:
field=str(filtersampleswin.cField.currentText())
value=str(filtersampleswin.tValue.text())
newname=str(filtersampleswin.tNewName.text())
overwrite=filtersampleswin.cOverwrite.checkState()
exact=filtersampleswin.cExact.checkState()
newexp=hs.sortbyfreq(cexp,field,value,exact=exact)
if overwrite==0:
newexp.studyname=newname
self.addexp(newexp)
else:
self.replaceexp(newexp)
def sortsamples(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
sortsampleswin = SortSamplesWindow(cexp)
res=sortsampleswin.exec_()
if res==QtWidgets.QDialog.Accepted:
field=str(sortsampleswin.cField.currentText())
newname=str(sortsampleswin.tNewName.text())
cnumeric=sortsampleswin.cNumeric.checkState()
if cnumeric==0:
numeric=False
else:
numeric=True
overwrite=sortsampleswin.cOverwrite.checkState()
newexp=hs.sortsamples(cexp,field=field,numeric=numeric)
if overwrite==0:
newexp.studyname=newname
self.addexp(newexp)
else:
self.replaceexp(newexp)
def clusterbacteria(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
val,ok=QtWidgets.QInputDialog.getInt(self,'Cluster Bacteria','Minimal number of reads per bacteria',10,0,10000)
if ok:
newexp=hs.clusterbacteria(cexp,minreads=val)
newexp.studyname=newexp.studyname+'_cb'
self.addexp(newexp)
def bicluster(self):
items=self.bMainList.selectedItems()
if len(items)!=1:
print("Need 1 item")
return
for citem in items:
cname=str(citem.text())
cexp=self.explist[cname]
biclusterwin = BiClusterWindow(cexp,cdb=self.cooldb,bdb=self.bactdb)
res=biclusterwin.exec_()
if res==QtWidgets.QDialog.Accepted:
newexp=hs.reorderbacteria(cexp,cexp.bactorder)