def updateinfo(self,csamp,cseq):
"""
update the information about the sample/bacteria
"""
self.csamp=csamp
self.cseq=cseq
self.lSample.setText(self.cexp.samples[self.csamp])
self.lTaxonomy.setText(self.cexp.tax[self.cseq])
self.lID.setText(str(self.cexp.sids[self.cseq]))
self.lReads.setText('%f' % (float(self.cexp.data[self.cseq,self.csamp])/100))
self.lSampleFieldVal.setText(self.cexp.smap[self.cexp.samples[self.csamp]][str(self.cSampleField.currentText())])
# update the stats about the database:
if self.cexp.seqdb:
self.lStudies.clear()
totappear,numstudies,allstudies,studysamples,totdbsamples=bactdb.GetSeqInfo(self.cexp.seqdb,self.cexp.seqs[self.cseq])
if totappear>0:
self.lNumSamples.setText(str('%d/%dK' % (totappear,int(totdbsamples/1000))))
self.lNumStudies.setText(str(numstudies))
res=studysamples.items()
vlens=[]
for cv in res:
totsamps=bactdb.SamplesInStudy(self.cexp.seqdb,cv[0])
vlens.append(float(len(cv[1]))/len(totsamps))
sv,si=au.isort(vlens,reverse=True)
for cind in si:
studyname=bactdb.StudyNameFromID(self.cexp.seqdb,res[cind][0])
self.lStudies.addItem('%s (%f)' % (studyname,vlens[cind]))
if self.FigureTab.currentIndex()==2:
self.plotxgraph()
if self.FigureTab.currentIndex()==1:
self.plotontology()
def GetSeqListInfo(db,seqs,info='samples'):
"""
Get information about a sequence list.
input:
db
seqs - a list of sequences (ACGT)
info - the info type to collect:
'samples' - the samples for each sequence
'studies' - the studies where each seq appears
'types' - env_matter+host_taxid
output:
res - a dict with info type as keys, each containing an array (1 entry per sequence) with the freq of the seq in the entry
"""
res={}
studyreads={}
for idx,cseq in enumerate(seqs):
if info=='samples':
# Get the read vector for the samples
pv=GetSeqVec(db,cseq)
if len(pv)==0:
continue
nz=np.where(pv>db.MINFREQ)
totalappear=len(nz[0])
au.Debug(2,"--------Seq",cseq)
au.Debug(3,"Found in",totalappear,"Samples")
au.Debug(3,"Fraction=",float(totalappear)/len(pv))
for csamp in nz[0]:
res.setdefault(csamp,np.zeros(len(seqs)))[idx]=pv[csamp]
elif info=='studies':
totappear,numstudies,allstudies,studysamples,totdbsamples=GetSeqInfo(db,cseq)
if totappear>0:
sres=studysamples.items()
vlens=[]
for cv in sres:
cstudy=cv[0]
cnumreads=cv[1]
if not cstudy in studyreads:
studyreads[cstudy]=SamplesInStudy(db,cstudy)
totsamps=studyreads[cstudy]
vlens.append(float(len(cnumreads))/len(totsamps))
sv,si=au.isort(vlens,reverse=True)
for cind in si:
studyid=sres[cind][0]
if vlens[cind]>0.25:
res.setdefault(studyid,np.zeros(len(seqs)))[idx]+=1
elif info=='types':
pv=GetSeqVec(db,cseq)
if len(pv)==0:
continue
nz=np.where(pv>db.MINFREQ)
for csamp in nz[0]:
db.cur.execute("SELECT Field,Value FROM Maps WHERE SampleID=?",[int(csamp)+1])
allvals=db.cur.fetchall()
matter='NA'
host='NA'
for cv in allvals:
if cv[0].lower()=='env_matter':
matter=cv[1]
if cv[0].lower()=='host_taxid':
host=cv[1]
res.setdefault(matter+'-'+host,np.zeros(len(seqs)))[idx]+=1
else:
au.Debug(9,"info type not supported",info)
return False
return res