from Portal.hvp.models.search.Variant import Variant
from Portal.hvp.models.search.HG_Build import HG_Build
from Portal.search.hgvs_parser.Validator import Validator
from Portal.search.hgvs_parser.Parser import Parser
# mutalyzer soap url
URL = 'https://mutalyzer.nl/services/?wsdl'
# get genomic build number
hg_build = HG_Build.objects.all()[0].BuildNumber
# get all variants
variant_list = Variant.objects.all()
# extract all the variants cDNA, refseq, refseqver and output to txt file
v = Validator()
file = open('input.txt', 'w')
for variant in variant_list:
if v.validate(variant.cDNA):
file.write(variant.Gene.RefSeqName + '.' + variant.Gene.RefSeqVer +
':' + variant.cDNA + '\n')
file.close()
# encode file to base64 binary
encoded = open('input.txt', 'rb').read().encode("base64")
print 'Connecting to web services...'
c = Client(URL, cache=None)
o = c.service
def variant_patient_view(request, geneID, variantID, instanceID, path_filter, path_filter_ratio):
template = 'variant_patient'
if not request.user.is_authenticated():
return render_to_response('home/timeout.html')
if request.user.get_profile().AccessStatus.ID != 2:
return render_to_response('home/permission.html', {'user': request.user})
gene = get_object_or_404(Gene, pk = geneID)
instance = get_object_or_404(VariantInstance, pk = instanceID)
searched_variant = ''
searched_variant_safe = ''
variant_query_string = ''
params = [instance.Patient_id]
page_error = False
search_tooshort = False
invalid_variant = False
# apply path filters
dict_path = Dict_path_filter(path_filter)
# apply path filter
path_id = Path_ID(path_filter)
# apply path filters ratio (the total number of instance per path)
dict_path_ratio = Dict_path_filter(path_filter_ratio)
# apply path filter ratio
path_ratio_id = Path_ID(path_filter_ratio)
# query options to filter by community consensus path
path_query_string = ''
if path_id != '':
if path_id == 'NULL':
path_query_string = ' and v.Pathogenicity_id is NULL '
else:
path_query_string = ' and v.Pathogenicity_id = %s '
params.append(path_id)
# search results
if 'search' in request.POST:
search_type = 'variantType' #request.POST['search_type']
if request.POST['searched_variant'] != '':
searched_variant = request.POST['searched_variant']
seached_variant_safe = searched_variant # url friendly
searched_variant = urllib.unquote(searched_variant) # raw form
validator = Validator()
if validator.validate(searched_variant) == False:
page_error = True
invalid_variant = True
# if there are no errors then proceed with the query
if not page_error:
parser = Parser()
variant = parser.parse('', searched_variant)
# query options filter by community consensus path
path_query_string = ''
variant_query_string = VariantQueryString(variant, params)
# query options filter by path count
count_query_string = ''
order_query_string = ' order by Instances desc '
if path_ratio_id != '':
count_query_string = """, (select count(hvp_variantinstance.Pathogenicity_id) as path
from hvp_variantinstance
where hvp_variantinstance.Variant_ID = v.ID
and hvp_variantinstance.pathogenicity_id = """ + str(path_ratio_id) + ') as Path_Count '
order_query_string = ' order by Path_Count desc '
query = """select v.*, hvp_variantinstance.Patient_id,
(select Count(hvp_variantinstance.Variant_id) as i from hvp_variantinstance
left join hvp_variant on hvp_variantinstance.Variant_ID = hvp_variant.ID
where hvp_variant.ID = v.ID) as instances """ + count_query_string + """
from hvp_variant v
left join hvp_variantinstance on v.ID = hvp_variantinstance.Variant_id
where hvp_variantinstance.Patient_id = %s
""" + path_query_string + variant_query_string + ' group by ID ' + order_query_string
qs = Variant.objects.raw(query, params)
variant_list = list(qs)
# sum of total results used to display on screen
results = len(variant_list)
# sets the paginator with the list of objects and number objects per page
paginator = Paginator(variant_list, 10)
# gets the current page
page = request.GET.get('page')
try:
variants = paginator.page(page)
except PageNotAnInteger:
variants = paginator.page(1)
except EmptyPage:
variants = paginator.page(paginator.num_pages)
return render_to_response('search/variant.html',
{
'user': request.user,
'template': template,
'dict_path': dict_path,
'path_filter': path_filter,
'geneID': geneID,
'variantID': variantID,
'gene': gene,
'variants': variants,
'instance': instance,
'results': results,
'page_error': page_error,
'search_tooshort': search_tooshort,
'invalid_variant': invalid_variant,
'searched_variant': searched_variant,
'searched_variant_safe': searched_variant_safe,
'dict_path_ratio': dict_path_ratio,
'path_filter_ratio': path_filter_ratio,
})
from Portal.hvp.models.search.Variant import Variant
from Portal.hvp.models.search.HG_Build import HG_Build
from Portal.search.hgvs_parser.Validator import Validator
from Portal.search.hgvs_parser.Parser import Parser
# mutalyzer soap url
URL = 'https://mutalyzer.nl/services/?wsdl'
# get genomic build number
hg_build = HG_Build.objects.all()[0].BuildNumber
# get all variants
variant_list = Variant.objects.all()
# extract all the variants cDNA, refseq, refseqver and output to txt file
v = Validator()
file = open('input.txt', 'w')
for variant in variant_list:
if v.validate(variant.cDNA):
file.write(variant.Gene.RefSeqName + '.' + variant.Gene.RefSeqVer + ':' + variant.cDNA + '\n')
file.close()
# encode file to base64 binary
encoded = open('input.txt', 'rb').read().encode("base64")
print 'Connecting to web services...'
c = Client(URL, cache=None)
o = c.service
def variant_results_view(request, geneID, searched_variant, search_type, path_filter, path_filter_ratio):
template = 'variant_result'
if not request.user.is_authenticated():
return render_to_response('home/timeout.html')
if request.user.get_profile().AccessStatus.ID != 2:
return render_to_response('home/permission.html', {'user': request.user})
# searching/filtering for a specific variant search
if 'search' in request.POST:
if request.POST['searched_variant'] != '':
#search_type = request.POST['search_type']
search_type = "variantType"
searched_variant = request.POST['searched_variant']
return HttpResponseRedirect('/search/gene/' + geneID +
'/searchvariant/' +
urllib.quote(searched_variant) +
'/' + search_type + '/results/' + path_filter +
'/' + path_filter_ratio + '/')
else:
# go back to the default variant page that lists all variants
return HttpResponseRedirect('/search/gene/' + geneID +
'/searchvariant/path_all/path_all/')
gene = get_object_or_404(Gene, pk = geneID)
geneName = gene.GeneName
page_error = False
search_tooShort = False
invalid_variant = False
# apply path filters
dict_path = Dict_path_filter(path_filter)
# apply path filter
path_id = Path_ID(path_filter)
# apply path filters ratio (the total number of instance per path)
dict_path_ratio = Dict_path_filter(path_filter_ratio)
# apply path filter ratio
path_ratio_id = Path_ID(path_filter_ratio)
# keep url safe version for path filter links
searched_variant_safe = searched_variant
# converting url string back to a proper variant nomenclature
searched_variant = urllib.unquote(searched_variant)
# search_type = searchType
paginate_results = 5
# check if the search query string is less than 2 characters, if so return error message to user
if len(searched_variant) < 2:
page_error = True
search_tooShort = True
# check if the entered variant is valid
validator = Validator()
if validator.validate(searched_variant) == False:
page_error = True
invalid_variant = True
# if there are no errors then proceed with the query
variant_list = []
variants = None
results = None
if not page_error:
# Break down the searched_variant using variant_parser to use in search with solr
# NB: I noticed that any values that have been broken down in the parser that
# has a '+' or '-' will be converted to a long int.
parser = Parser()
variant = parser.parse('', searched_variant)
# query options filter by community consensus path
path_query_string = ''
params = [geneName]
variant_query_string = VariantQueryString(variant, params)
if path_id != '':
if path_id == 'NULL':
path_query_string = ' and v.Pathogenicity_id is NULL '
else:
path_query_string = ' and v.Pathogenicity_id = %s '
params.append(path_id)
# query options filter by path count
count_query_string = ''
order_query_string = ' order by Instances desc '
if path_ratio_id != '':
count_query_string = """, (select count(hvp_variantinstance.Pathogenicity_id) as path
from hvp_variantinstance
where hvp_variantinstance.Variant_ID = v.ID
and hvp_variantinstance.pathogenicity_id = """ + str(path_ratio_id) + ') as Path_Count '
order_query_string = ' order by Path_Count desc '
query = 'select v.*, Count(hvp_variantinstance.Variant_id) as Instances' + count_query_string + """
from hvp_variant v
left join hvp_variantinstance on v.ID = hvp_variantinstance.Variant_id
left join hvp_gene on v.Gene_id = hvp_gene.ID
where hvp_gene.GeneName = %s
""" + path_query_string + variant_query_string + ' group by ID ' + order_query_string
qs = Variant.objects.raw(query, params)
variant_list = list(qs)
# sum of total results used to display on screen
results = variant_list.count #len(variant_list)
# sets the paginator with the list of objects and number of objects per page
paginator = Paginator(variant_list, 10)
# gets the current page
page = request.GET.get('page')
try:
variants = paginator.page(page)
except PageNotAnInteger:
variants = paginator.page(1)
except EmptyPage:
variants = paginator.page(paginator.num_pages)
return render_to_response('search/variant.html',
{
'user': request.user,
'template': template,
'searched_variant': searched_variant,
'searched_variant_safe': searched_variant_safe,
'page_error': page_error,
'invalid_variant': invalid_variant,
'paginate_results': paginate_results,
'geneName' : geneName,
'geneID' : geneID,
'search_type': search_type,
'variants': variants,
'results': results,
'search_tooShort': search_tooShort,
'path_filter': path_filter,
'dict_path': dict_path,
'dict_path_ratio': dict_path_ratio,
'path_filter_ratio': path_filter_ratio,
},
context_instance=RequestContext(request))