def search(request):
if request.GET.has_key('q'):
try:
q = request.GET['q']
results = s.search(q)
gene_ids= []
for result in results:
if result['doc_type'] == 'GENE':
gene_ids.append(result['id'])
gene_objs = Gene.objects.filter(pk__in=gene_ids)
species_genes = {}
species_names = {}
genes = []
for gene_obj in gene_objs:
species_names[gene_obj.species.id] = gene_obj.species.name
bicluster_ids = [b.id for b in gene_obj.bicluster_set.all()]
regulates = Bicluster.objects.filter(influences__name__contains=gene_obj.name)
_, influence_biclusters = get_influence_biclusters(gene_obj)
if not species_genes.has_key(gene_obj.species.id):
species_genes[gene_obj.species.id] = []
genes = species_genes[gene_obj.species.id]
genes.append(GeneResultEntry(gene_obj.id, gene_obj.name,
gene_obj.species.id,
gene_obj.description,
bicluster_ids,
influence_biclusters,
regulates))
except Exception as e:
error_message = str(e)
return render_to_response('search.html', locals())
def search(request):
if request.GET.has_key('q'):
try:
q = request.GET['q']
results = s.search(q)
gene_ids = []
for result in results:
if result['doc_type'] == 'GENE':
gene_ids.append(result['id'])
gene_objs = Gene.objects.filter(pk__in=gene_ids)
species_genes = {}
species_names = {}
genes = []
for gene_obj in gene_objs:
species_names[gene_obj.species.id] = gene_obj.species.name
bicluster_ids = [b.id for b in gene_obj.bicluster_set.all()]
regulates = Bicluster.objects.filter(
influences__name__contains=gene_obj.name)
_, influence_biclusters = get_influence_biclusters(gene_obj)
if not species_genes.has_key(gene_obj.species.id):
species_genes[gene_obj.species.id] = []
genes = species_genes[gene_obj.species.id]
genes.append(
GeneResultEntry(gene_obj.id, gene_obj.name,
gene_obj.species.id, gene_obj.description,
bicluster_ids, influence_biclusters,
regulates))
except Exception as e:
error_message = str(e)
return render_to_response('search.html', locals())
def gene(request, gene=None, network_id=None):
if request.GET.has_key("view"):
view = request.GET["view"]
else:
view = ""
if gene:
try:
gene_id = int(gene)
gene = Gene.objects.get(id=gene_id)
except ValueError:
gene = find_gene_by_name(gene)
elif request.GET.has_key("id"):
gene_id = request.GET["id"]
gene = Gene.objects.get(id=gene_id)
else:
gene_count = Gene.objects.count()
species_count = Species.objects.count()
return render_to_response("genes_empty.html", locals())
# TODO: need to figure out how to handle cases where there's more than one network
if network_id:
network_id = int(network_id)
elif gene.species.network_set.count() > 0:
network = gene.species.network_set.all()[0]
network_id = network.id
else:
network_id = None
member_biclusters, influence_biclusters = get_influence_biclusters(gene)
# set species for use in template
species = gene.species
# get neighbor genes
neighbor_genes = gene.neighbor_genes(network_id)
# compile functions into groups by functional system
systems = []
for key, functions in gene.functions_by_type().items():
system = {}
system["name"] = functional_systems[key].display_name
system["functions"] = [
'(<a href="%s">%s</a>) %s' % (function.link_to_term(), function.native_id, function.name)
for function in functions
]
systems.append(system)
# if the gene is a transcription factor, how many biclusters does it regulate?
count_regulated_biclusters = gene.count_regulated_biclusters(network_id)
# regulated_biclusters = Bicluster.objects.distinct().filter(influences__name__contains=gene.name)
regulated_biclusters = gene.regulated_biclusters(network_id)
bicluster_pssms = {}
preview_motifs = []
all_motifs = []
for mbicl in member_biclusters:
motifs = mbicl.motif_set.all()
all_motifs.extend(motifs)
pssms = __make_pssms(motifs)
preview_added = False
for motif_id, pssm in pssms.items():
bicluster_pssms[motif_id] = pssm
if not preview_added:
preview_motifs.append(motif_id)
preview_added = True
motifs = all_motifs # used in template
preview_motifs = preview_motifs[:2] # restrict to 2 motifs on the front tab to improve load time
if request.GET.has_key("format"):
format = request.GET["format"]
if format == "html":
return render_to_response("gene_snippet.html", locals())
return render_to_response("gene.html", locals())
def gene(request, gene=None, network_id=None):
if request.GET.has_key('view'):
view = request.GET['view']
else:
view = ""
if gene:
try:
gene_id = int(gene)
gene = Gene.objects.get(id=gene_id)
except ValueError:
gene = find_gene_by_name(gene)
elif request.GET.has_key('id'):
gene_id = request.GET['id']
gene = Gene.objects.get(id=gene_id)
else:
gene_count = Gene.objects.count()
species_count = Species.objects.count()
return render_to_response('genes_empty.html', locals())
# TODO: need to figure out how to handle cases where there's more than one network
if network_id:
network_id = int(network_id)
elif gene.species.network_set.count() > 0:
network = gene.species.network_set.all()[0]
network_id = network.id
else:
network_id = None
member_biclusters, influence_biclusters = get_influence_biclusters(gene)
# set species for use in template
species = gene.species
# get neighbor genes
neighbor_genes = gene.neighbor_genes(network_id)
# compile functions into groups by functional system
systems = []
for key, functions in gene.functions_by_type().items():
system = {}
system['name'] = functional_systems[key].display_name
system['functions'] = [ "(<a href=\"%s\">%s</a>) %s" % (function.link_to_term(), function.native_id, function.name,) \
for function in functions ]
systems.append(system)
# if the gene is a transcription factor, how many biclusters does it regulate?
count_regulated_biclusters = gene.count_regulated_biclusters(network_id)
#regulated_biclusters = Bicluster.objects.distinct().filter(influences__name__contains=gene.name)
regulated_biclusters = gene.regulated_biclusters(network_id)
bicluster_pssms = {}
preview_motifs = []
all_motifs = []
for mbicl in member_biclusters:
motifs = mbicl.motif_set.all()
all_motifs.extend(motifs)
pssms = __make_pssms(motifs)
preview_added = False
for motif_id, pssm in pssms.items():
bicluster_pssms[motif_id] = pssm
if not preview_added:
preview_motifs.append(motif_id)
preview_added = True
motifs = all_motifs # used in template
preview_motifs = preview_motifs[:
2] # restrict to 2 motifs on the front tab to improve load time
if request.GET.has_key('format'):
format = request.GET['format']
if format == 'html':
return render_to_response('gene_snippet.html', locals())
return render_to_response('gene.html', locals())