def family_group_gene(request, project_id, family_group_slug, gene_id):
project = get_object_or_404(Project, project_id=project_id)
family_group = get_object_or_404(FamilyGroup,
project=project,
slug=family_group_slug)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
gene_id = get_gene_id_from_str(gene_id, get_reference())
gene = get_reference().get_gene(gene_id)
varfilter = get_default_variant_filter(
'all_coding',
mall.get_annotator().reference_population_slugs)
variants_by_family = family_group_analysis.get_variants_in_gene(
family_group, gene_id, variant_filter=varfilter)
return render(
request, 'family_group/family_group_gene.html', {
'project': project,
'family_group': family_group,
'family_group_json': json.dumps(family_group.toJSON()),
'gene_json': json.dumps(gene),
'gene': gene,
'variants_by_family_json': json.dumps(variants_by_family),
})
def get_gene_id_list_from_raw(raw_text, reference):
"""
raw_text is a string that contains a list of genes separated by whitespace
return (success, result)
if success is true, result is a list of gene_ids that can be used in a variant_filter
if false, result is a gene_id that could not be converted
"""
gene_strs = raw_text.split()
gene_ids = []
for gene_str in gene_strs:
if xbrowse_utils.get_gene_id_from_str(gene_str, reference):
gene_ids.append(xbrowse_utils.get_gene_id_from_str(gene_str, reference))
else:
return False, gene_str
return True, gene_ids
def get_gene_id_list_from_raw(raw_text, reference):
"""
raw_text is a string that contains a list of genes separated by whitespace
return (success, result)
if success is true, result is a list of gene_ids that can be used in a variant_filter
if false, result is a gene_id that could not be converted
"""
gene_strs = raw_text.split()
gene_ids = []
for gene_str in gene_strs:
if xbrowse_utils.get_gene_id_from_str(gene_str, reference):
gene_ids.append(xbrowse_utils.get_gene_id_from_str(gene_str, reference))
else:
return False, gene_str
return True, gene_ids
def gene_info(request, gene_str):
real_gene_id = get_gene_id_from_str(gene_str, get_reference())
gene = get_reference().get_gene(real_gene_id)
gene['expression'] = get_reference().get_tissue_expression_display_values(real_gene_id)
gene_json = json.dumps(gene)
return render(request, 'gene_info.html', {
'gene_json': gene_json,
'gene_symbol': gene['symbol'],
})
def gene_info(request, gene_str):
real_gene_id = get_gene_id_from_str(gene_str, get_reference())
gene = get_reference().get_gene(real_gene_id)
gene['expression'] = get_reference().get_tissue_expression_display_values(
real_gene_id)
gene_json = json.dumps(gene)
return render(request, 'gene_info.html', {
'gene_json': gene_json,
'gene_symbol': gene['symbol'],
})
def gene_info(request, gene_str):
real_gene_id = get_gene_id_from_str(gene_str, get_reference())
gene = get_reference().get_gene(real_gene_id)
gene['expression'] = get_reference().get_tissue_expression_display_values(real_gene_id)
add_notes_to_genes([gene], request.user)
gene_json = json.dumps(gene)
return render(request, 'gene_info.html', {
'gene_json': gene_json,
'gene_symbol': gene['symbol'],
'new_page_url': '/gene_info/{}'.format(gene_str),
})
def gene_info(request, gene_str):
real_gene_id = get_gene_id_from_str(gene_str, get_reference())
gene = get_reference().get_gene(real_gene_id)
gene['expression'] = get_reference().get_tissue_expression_display_values(
real_gene_id)
add_notes_to_genes([gene], request.user)
gene_json = json.dumps(gene)
return render(
request, 'gene_info.html', {
'gene_json': gene_json,
'gene_symbol': gene['symbol'],
'new_page_url': '/gene_info/{}'.format(gene_str),
})
def clean(self):
cleaned_data = super(GeneListForm, self).clean()
gene_str_list = cleaned_data.get('genes', '').split()
gene_ids = []
gene_id_errors = []
for s in gene_str_list:
gene_id = get_gene_id_from_str(s.strip(), get_reference())
if not gene_id:
gene_id_errors.append(s)
gene_ids.append(gene_id)
if len(gene_id_errors) > 0:
raise forms.ValidationError("Can't find gene(s): %s" % ", ".join(gene_id_errors))
cleaned_data['gene_ids'] = gene_ids
cleaned_data['slug'] = slugify(cleaned_data['name'])[:40]
cleaned_data['is_public'] = cleaned_data['is_public'] == 'yes'
return cleaned_data
def clean(self):
cleaned_data = super(GeneListForm, self).clean()
gene_str_list = cleaned_data.get("genes", "").split()
gene_ids = []
gene_id_errors = []
for s in gene_str_list:
gene_id = get_gene_id_from_str(s.strip(), get_reference())
if not gene_id:
gene_id_errors.append(s)
gene_ids.append(gene_id)
if len(gene_id_errors) > 0:
raise forms.ValidationError("Can't find a gene ID for this gene: %s" % " and ".join(gene_id_errors))
cleaned_data["gene_ids"] = gene_ids
cleaned_data["slug"] = slugify(cleaned_data["name"])[:40]
cleaned_data["is_public"] = cleaned_data["is_public"] == "yes"
return cleaned_data
def clean(self):
cleaned_data = super(GeneListForm, self).clean()
gene_str_list = cleaned_data.get('genes', '').split()
gene_ids = []
gene_id_errors = []
for s in gene_str_list:
gene_id = get_gene_id_from_str(s.strip(), get_reference())
if not gene_id:
gene_id_errors.append(s)
gene_ids.append(gene_id)
if len(gene_id_errors) > 0:
raise forms.ValidationError("Can't find gene(s): %s" %
", ".join(gene_id_errors))
cleaned_data['gene_ids'] = gene_ids
cleaned_data['slug'] = slugify(cleaned_data['name'])[:40]
cleaned_data['is_public'] = cleaned_data['is_public'] == 'yes'
return cleaned_data
def family_group_gene(request, project_id, family_group_slug, gene_id):
project = get_object_or_404(Project, project_id=project_id)
family_group = get_object_or_404(FamilyGroup, project=project, slug=family_group_slug)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
gene_id = get_gene_id_from_str(gene_id, get_reference())
gene = get_reference().get_gene(gene_id)
varfilter = get_default_variant_filter('all_coding', mall.get_annotator().reference_population_slugs)
variants_by_family = family_group_analysis.get_variants_in_gene(family_group, gene_id, variant_filter=varfilter)
return render(request, 'family_group/family_group_gene.html', {
'project': project,
'family_group': family_group,
'family_group_json': json.dumps(family_group.toJSON()),
'gene_json': json.dumps(gene),
'gene': gene,
'variants_by_family_json': json.dumps(variants_by_family),
})
