def map_signature(request, pk):
signature = Signature.objects.get(pk=pk)
taxid = signature.species.taxid
transcripts = signature.transcripts.all()
taxid = signature.species.taxid
mapped = 0
transcript_count = transcripts.count()
counter = Counter(transcript_count)
#geneExpressions = GeneExpressions()
for transcript in transcripts:
counter.count()
gene_id = mapid(transcript.seq_id, taxid=taxid)
#print transcript, gene_id
if gene_id and isinstance(gene_id, int):
transcript.entrez_gene_id = gene_id
transcript.save()
#t = Transcript.objects.get(pk = transcript.pk)
#print("T: %s %s %s" % (t.pk, t.seq_id, t.entrez_gene_id))
#print transcript, transcript.entrez_gene_id
# if gene_id:
# gene, created = Gene.objects.get_or_create(id=gene_id, species_id=taxid)
# if gene_id not in geneExpressions:
# geneExpressions[gene_id] = GeneExpression(id, transcript, signature)
# else:
# geneExpressions[gene_id].add(transcript, signature)
# signature.genes.add(gene)
mapped += 1
msg = 'Mapped %s' % (100.*mapped/transcript_count)
messages.add_message(request, messages.INFO, _(msg))
#genes = signatures.genes.all()
return redirect('/expressions/signatures/')
def save(self, *args,
**kwargs): #TODO: must be splitted into several methods
if not self.pk:
self.mean = percentage(self.exp.mean, self.ctr.mean) or self.mean
self.median = percentage(self.exp.median,
self.ctr.median) or self.median
self.max = percentage(self.exp.max, self.ctr.max) or self.max
if self.exp.genotype:
interventions = Intervention.objects.filter(
name__icontains=self.exp.genotype)
elif self.exp.diet:
interventions = Intervention.objects.filter(
name__icontains=self.exp.diet)
else:
interventions = []
#Q(name__icontains=self.exp.genotype) | Q(name__icontains=self.ctr.genotype))
#print("%s %s %s" % (self.exp.genotype, self.ctr.genotype, interventions))
for intervention in interventions:
self.intervention = intervention
#print("mapping")
if self.exp.genotype:
if "/" in self.exp.genotype.name:
genotype = self.exp.genotype.name.split('/')[0]
else:
genotype = self.exp.genotype.name
if "(" in genotype:
genotype = genotype.split('(')[0].rstrip()
#print("map id")
#print(genotype)
id = mapid(genotype, self.exp.experiment.species.taxid)
#print("mapped")
else:
id = None
if id:
try:
factor = Factor.objects.get(entrez_gene_id=id)
interventions = factor.intervention.all()
if interventions:
self.intervention = interventions[0]
except ObjectDoesNotExist:
pass # Make message
#print("ObjectDoesNotExist %s" % id)
except MultipleObjectsReturned:
pass # Make message
#print("MultipleObjectsReturned %s" % id)
#print self.intervention
#else: factor = ''
#print("Mapped factor: %s = %s (%s) %s" % (genotype, id, factor, interventions))
super(Comparison, self).save(*args, **kwargs)
def save(self, *args, **kwargs):
if not self.pk:
self.mean = percentage(self.exp.mean, self.ctr.mean) or self.mean
self.median = percentage(self.exp.median, self.ctr.median) or self.median
self.max = percentage(self.exp.max, self.ctr.max) or self.max
if self.exp.genotype:
interventions = Intervention.objects.filter(name__icontains=self.exp.genotype)
elif self.exp.diet:
interventions = Intervention.objects.filter(name__icontains=self.exp.diet)
else:
interventions = []
#Q(name__icontains=self.exp.genotype) | Q(name__icontains=self.ctr.genotype))
#print("%s %s %s" % (self.exp.genotype, self.ctr.genotype, interventions))
for intervention in interventions:
self.intervention = intervention
#print("mapping")
if self.exp.genotype:
if "/" in self.exp.genotype.name:
genotype = self.exp.genotype.name.split('/')[0]
else:
genotype = self.exp.genotype.name
if "(" in genotype:
genotype = genotype.split('(')[0].rstrip()
#print("map id")
#print(genotype)
id = mapid(genotype, self.exp.experiment.species.taxid)
#print("mapped")
else:
id = None
if id:
try:
factor = Factor.objects.get(entrez_gene_id=id)
interventions = factor.intervention.all()
if interventions:
self.intervention = interventions[0]
except ObjectDoesNotExist:
pass # Make message
#print("ObjectDoesNotExist %s" % id)
except MultipleObjectsReturned:
pass # Make message
#print("MultipleObjectsReturned %s" % id)
#print self.intervention
#else: factor = ''
#print("Mapped factor: %s = %s (%s) %s" % (genotype, id, factor, interventions))
super(Comparison, self).save(*args, **kwargs)
def map_signature(request, pk):
signature = Signature.objects.get(pk=pk)
taxid = signature.species.taxid
transcripts = signature.transcripts.all()
taxid = signature.species.taxid
mapped = 0
transcript_count = transcripts.count()
counter = Counter(transcript_count)
#geneExpressions = GeneExpressions()
for transcript in transcripts:
counter.count()
gene_id = mapid(transcript.seq_id, taxid=taxid)
#print transcript, gene_id
if gene_id and isinstance(gene_id, int):
transcript.entrez_gene_id = gene_id
transcript.save()
#t = Transcript.objects.get(pk = transcript.pk)
#print("T: %s %s %s" % (t.pk, t.seq_id, t.entrez_gene_id))
#print transcript, transcript.entrez_gene_id
# if gene_id:
# gene, created = Gene.objects.get_or_create(id=gene_id, species_id=taxid)
# if gene_id not in geneExpressions:
# geneExpressions[gene_id] = GeneExpression(id, transcript, signature)
# else:
# geneExpressions[gene_id].add(transcript, signature)
# signature.genes.add(gene)
mapped += 1
msg = 'Mapped %s' % (100. * mapped / transcript_count)
messages.add_message(request, messages.INFO, _(msg))
#genes = signatures.genes.all()
return redirect('/expressions/signatures/')
#234567891123456789212345678931234567894123456789512345678961234567897123456789
def map_signatures(request):
print ("Initializing mapping.")
signatures = Signature.objects.all()
mapped = 0
total = 0
for signature in signatures:
print ("Signature: %s" % signature)
taxid = signature.species.taxid
transcripts = signature.transcripts.all()
transcript_count = transcripts.count()
total += transcript_count
counter = Counter(transcript_count)
for transcript in transcripts:
counter.count()
gene_id = mapid(str(transcript.seq_id), taxid=taxid)
if gene_id and isinstance(gene_id, int):
transcript.entrez_gene_id = gene_id
transcript.save()
mapped += 1
# print transcript, transcript.entrez_gene_id
msg = "Mapped %s" % (100.0 * mapped / total)
messages.add_message(request, messages.INFO, _(msg))
return redirect("/expressions/signatures/")
def map_signatures(request):
print("Initializing mapping.")
signatures = Signature.objects.all()
mapped = 0
total = 0
for signature in signatures:
if not "Timeless" in signature.name: continue
print("Signature: %s" % signature)
taxid = signature.species.taxid
transcripts = signature.transcripts.all()
transcript_count = transcripts.count()
total += transcript_count
counter = Counter(transcript_count)
for transcript in transcripts:
counter.count()
gene_id = mapid(str(transcript.seq_id), taxid=taxid)
if gene_id and isinstance(gene_id, int):
transcript.entrez_gene_id = gene_id
transcript.save()
mapped += 1
#print transcript, transcript.entrez_gene_id
msg = "Mapped %s" % (100. * mapped / total)
messages.add_message(request, messages.INFO, _(msg))
return redirect('/expressions/signatures/')