def filtertaxonomy(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=QtGui.QInputDialog.getText(self,'Filter taxonomy','Taxonomy to filter')
if ok:
newexp=hs.filtertaxonomy(cexp,tax=str(val),exact=False)
newexp.studyname=newexp.studyname+'_ftax'
self.addexp(newexp)
def cleantaxonomy(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]
ctwin = CleanTaxonomyWindow(cexp)
res=ctwin.exec_()
if res==QtGui.QDialog.Accepted:
newexp=hs.copyexp(cexp)
if ctwin.cMitochondria.checkState():
newexp=hs.filtertaxonomy(newexp,'mitochondria',exclude=True)
if ctwin.cChloroplast.checkState():
newexp=hs.filtertaxonomy(newexp,'Streptophyta',exclude=True)
newexp=hs.filtertaxonomy(newexp,'Chloroplast',exclude=True)
if ctwin.cUnknown.checkState():
newexp=hs.filtertaxonomy(newexp,'nknown',exclude=True)
if ctwin.cBacteria.checkState():
newexp=hs.filtertaxonomy(newexp,'Bacteria;',exclude=True,exact=True)
newexp=hs.normalizereads(newexp)
newexp.studyname=cexp.studyname+'.ct'
self.addexp(newexp)
def cleantaxonomy(expdat,mitochondria=True,chloroplast=True,bacteria=True,unknown=True,exclude=True):
"""
remove common non-16s sequences from the experiment and renormalize
input:
expdat : Experiment
mitochondria : bool
remove mitochondrial sequences
chloroplast : bool
remove chloroplast sequences
bacteria : bool
remove sequences only identified as "Bacteria" (no finer identification)
unknown : bool
remove unknown sequences
exclude : bool
True (default) to remove these sequecnes, False to keep them and throw other
output:
newexp : Experiment
the renormalized experiment without these bacteria
"""
params=locals()
newexp=hs.copyexp(expdat)
if mitochondria:
if exclude:
newexp=hs.filtertaxonomy(newexp,'mitochondria',exclude=True)
else:
ne1=hs.filtertaxonomy(newexp,'mitochondria',exclude=False)
if chloroplast:
if exclude:
newexp=hs.filtertaxonomy(newexp,'Streptophyta',exclude=True)
newexp=hs.filtertaxonomy(newexp,'Chloroplast',exclude=True)
else:
ne2=hs.filtertaxonomy(newexp,'Streptophyta',exclude=False)
ne3=hs.filtertaxonomy(newexp,'Chloroplast',exclude=False)
if unknown:
if exclude:
newexp=hs.filtertaxonomy(newexp,'Unknown',exclude=True)
newexp=hs.filtertaxonomy(newexp,'Unclassified;',exclude=True,exact=True)
else:
ne4=hs.filtertaxonomy(newexp,'Unknown',exclude=False)
ne5=hs.filtertaxonomy(newexp,'Unclassified;',exclude=False,exact=True)
if bacteria:
if exclude:
newexp=hs.filtertaxonomy(newexp,'Bacteria;',exclude=True,exact=True)
else:
ne6=hs.filtertaxonomy(newexp,'Bacteria;',exclude=False,exact=True)
if exclude:
newexp=hs.normalizereads(newexp)
else:
allseqs=[]
allseqs+=(ne1.seqs)
allseqs+=(ne2.seqs)
allseqs+=(ne3.seqs)
allseqs+=(ne4.seqs)
allseqs+=(ne5.seqs)
allseqs+=(ne6.seqs)
allseqs=list(set(allseqs))
newexp=hs.filterseqs(newexp,allseqs)
newexp.filters.append('Clean Taxonomy (remove mitochondria etc.)')
hs.addcommand(newexp,"cleantaxonomy",params=params,replaceparams={'expdat':expdat})
hs.Debug(6,'%d sequences before filtering, %d after' % (len(expdat.seqs),len(newexp.seqs)))
return newexp
