except suds.WebFault as e:
resultFinished = False
except:
resultFinished = False
# decode results
decoded = base64.b64decode(encodedResults)
#write results to file for referencing/debugging
file = open('result.txt', 'w')
file.write(decoded)
file.close()
# write genomic results back into database hvp_variant table
results_list = decoded.splitlines()
parser = Parser()
# extract the data from results
for result in results_list:
# skip the header on the first line
if 'Input Variant' not in result:
# split the line up by 'tabs'
line = re.split(r'\t+', result)
# original values submitted
cDNA_value = line[0].split(':')
cDNA_ref = cDNA_value[0]
cDNA_ref_split = cDNA_ref.split('.')
cDNA_refName = cDNA_ref_split[0]
cDNA_refVer = cDNA_ref_split[1]
cDNA_var = cDNA_value[1]
except suds.WebFault as e:
resultFinished = False
except:
resultFinished = False
# decode results
decoded = base64.b64decode(encodedResults)
#write results to file for referencing/debugging
file = open('result.txt', 'w')
file.write(decoded)
file.close()
# write genomic results back into database hvp_variant table
results_list = decoded.splitlines()
parser = Parser()
# extract the data from results
for result in results_list:
# skip the header on the first line
if 'Input Variant' not in result:
# split the line up by 'tabs'
line = re.split(r'\t+', result)
# original values submitted
cDNA_value = line[0].split(':')
cDNA_ref = cDNA_value[0]
cDNA_ref_split = cDNA_ref.split('.')
cDNA_refName = cDNA_ref_split[0]
cDNA_refVer = cDNA_ref_split[1]
cDNA_var = cDNA_value[1]
def gene_results_view(request):
# send user to timeout page if not authenticated
if not request.user.is_authenticated():
return render_to_response('home/timeout.html')
# deny access if permission has not been granted
if request.user.get_profile().AccessStatus.ID != 2:
return render_to_response('home/permission.html',
{'user': request.user})
# default if blank search all
searched_gene = ''
if 'searched_gene' in request.POST:
searched_gene = request.POST['searched_gene']
#gene = searchedGene
paginate_results = 5
error = False
# if searched_gene is genomic variant starting with "chr."(chromosome) or 'nc_'(refseq)
# then we can go directy to the gene and searched for the variant in the variant page.
if ('chr' in searched_gene.lower() or 'nc_'
in searched_gene.lower()) and ':' in searched_gene.lower():
# try and get the gene from the variant
try:
p = Parser()
variant = p.parse('', searched_gene)
variant.genomic_ref
variant_list = []
if 'nc_' in searched_gene.lower():
split_string = searched_gene.lower().split(':')[0].split(
'.')[0]
variant_list = Variant.objects.filter(
GenomicRefSeq=split_string)
else:
split_string = searched_gene.lower().split(':')[0].replace(
'chr', '')
variant_list = Variant.objects.filter(
Q(GenomicRefSeq__contains=split_string))
if variant_list >= 1:
gene = variant_list[0].Gene
return HttpResponseRedirect(
'/search/gene/' + str(gene.ID) + '/searchvariant/' +
urllib.quote(searched_gene) +
'/variantType/results/path_all/path_all/')
except:
error = True
# tries for a precise search for the GeneName, groups then by GeneName due to duplicate GeneNames
# with different RefSeq Names and Versions.
if searched_gene == '':
query = """
select g1.*, max(hvp_variantinstance.DateSubmitted) as DateSubmitted,
(select Count(hvp_variant.ID) as variants from hvp_variant
left join hvp_gene g2 on hvp_variant.Gene_id = g2.ID
where g2.GeneName = g1.GeneName) as Variants,
(select Count(hvp_variantinstance.ID) as variantInstances from hvp_variantinstance
left join hvp_variant on hvp_variantinstance.Variant_id = hvp_variant.ID
left join hvp_gene on hvp_variant.Gene_id = hvp_gene.ID
where hvp_gene.GeneName = g1.GeneName) as VariantInstances
from hvp_gene g1
left join hvp_variant on g1.ID = hvp_variant.Gene_id
left join hvp_variantinstance on hvp_variant.ID = hvp_variantinstance.Variant_id
group by GeneName
order by GeneName asc
"""
qs = Gene.objects.raw(query)
gene_list = list(qs)
else:
query = """
select g1.*, max(hvp_variantinstance.DateSubmitted) as DateSubmitted,
(select Count(hvp_variant.ID) as variants from hvp_variant
left join hvp_gene g2 on hvp_variant.Gene_id = g2.ID
where g2.GeneName = g1.GeneName) as Variants,
(select Count(hvp_variantinstance.ID) as variantInstances from hvp_variantinstance
left join hvp_variant on hvp_variantinstance.Variant_id = hvp_variant.ID
left join hvp_gene on hvp_variant.Gene_id = hvp_gene.ID
where hvp_gene.GeneName = g1.GeneName) as VariantInstances
from hvp_gene g1
left join hvp_variant on g1.ID = hvp_variant.Gene_id
left join hvp_variantinstance on hvp_variant.ID = hvp_variantinstance.Variant_id
where GeneName like %s
group by GeneName
order by GeneName asc
"""
qs = Gene.objects.raw(query, [searched_gene + '%'])
gene_list = list(qs)
# if nothing is return then we need to search in the other areas
if len(gene_list) == 0:
query = """
select g1.*, max(hvp_variantinstance.DateSubmitted) as DateSubmitted,
(select Count(hvp_variant.ID) as variants from hvp_variant
left join hvp_gene g2 on hvp_variant.Gene_id = g2.ID
where g2.GeneName = g1.GeneName) as Variants,
(select Count(hvp_variantinstance.ID) as variantInstances from hvp_variantinstance
left join hvp_variant on hvp_variantinstance.Variant_id = hvp_variant.ID
left join hvp_gene on hvp_variant.Gene_id = hvp_gene.ID
where hvp_gene.GeneName = g1.GeneName) as VariantInstances
from hvp_gene g1
left join hvp_variant on g1.ID = hvp_variant.Gene_id
left join hvp_variantinstance on hvp_variant.ID = hvp_variantinstance.Variant_id
where (RefSeqName like %s or GeneDescription like %s or HGNC_ID like %s
or AlternateSymbols like %s or AlternateNames like %s or Chromosome like %s
or PreviousSymbols like %s or PreviousNames like %s)
group by GeneName
order by GeneName asc
"""
qs = Gene.objects.raw(query, [
searched_gene + '%', '%' + searched_gene + '%',
searched_gene + '%', '%' + searched_gene + '%',
'%' + searched_gene + '%', searched_gene + '%',
'%' + searched_gene + '%', '%' + searched_gene + '%'
])
gene_list = list(qs)
# if still nothing then look at the gene disease tags - using taggit
if len(gene_list) == 0:
# break down string into list
searched_gene_list = searched_gene.split(' ')
gene_list = Gene.objects.filter(
DiseasesTags__name__in=searched_gene_list).distinct()
# number genes returned from search
gene_count = gene_list.count
# sets the paginator with the list of objects and number of objects per page
paginator = Paginator(gene_list, 10)
# gets the current page
page = request.GET.get('page')
try:
genes = paginator.page(page)
except PageNotAnInteger:
genes = paginator.page(1)
except EmptyPage:
genes = paginator.page(paginator.num_pages)
return render_to_response('search/gene_result.html', {
'user': request.user,
'error': error,
'searched_gene': searched_gene,
'gene_count': gene_count,
'genes': genes,
'paginate_results': paginate_results,
},
context_instance=RequestContext(request))
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,
})
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))
# path where Portal django app is located, this usually 1 directory up from
# where the app sits. e.g: '/path/location/Portal' then put down '/path/location'
path = ''
sys.path.append(path)
os.environ['DJANGO_SETTINGS_MODULE'] = 'Portal.settings'
from Portal import settings
setup_environ(settings)
from Portal.hvp.models.search.Gene import Gene
from Portal.hvp.models.search.Variant import Variant
from Portal.search.hgvs_parser.Parser import Parser
# get all variants
variant_list = Variant.objects.all()
parser = Parser()
for variant in variant_list:
if variant.cDNA != 'None':
try:
v = parser.parse('', variant.cDNA)
if v.position:
variant.Position = v.position.replace('*','')
if v.position_intron:
variant.PositionIntron = v.position_intron.replace('*','')
else:
if v.range_lower:
variant.LowerRange = v.range_lower.replace('*','')
if v.range_lower_intron:
def gene_results_view(request):
# send user to timeout page if not authenticated
if not request.user.is_authenticated():
return render_to_response('home/timeout.html')
# deny access if permission has not been granted
if request.user.get_profile().AccessStatus.ID != 2:
return render_to_response('home/permission.html', { 'user': request.user })
# default if blank search all
searched_gene = ''
if 'searched_gene' in request.POST:
searched_gene = request.POST['searched_gene']
#gene = searchedGene
paginate_results = 5
error = False
# if searched_gene is genomic variant starting with "chr."(chromosome) or 'nc_'(refseq)
# then we can go directy to the gene and searched for the variant in the variant page.
if ('chr' in searched_gene.lower() or 'nc_' in searched_gene.lower()) and ':' in searched_gene.lower():
# try and get the gene from the variant
try:
p = Parser()
variant = p.parse('', searched_gene)
variant.genomic_ref
variant_list = []
if 'nc_' in searched_gene.lower():
split_string = searched_gene.lower().split(':')[0].split('.')[0]
variant_list = Variant.objects.filter(GenomicRefSeq = split_string)
else:
split_string = searched_gene.lower().split(':')[0].replace('chr','')
variant_list = Variant.objects.filter(Q(GenomicRefSeq__contains=split_string))
if variant_list >= 1:
gene = variant_list[0].Gene
return HttpResponseRedirect('/search/gene/' + str(gene.ID) + '/searchvariant/' +
urllib.quote(searched_gene) + '/variantType/results/path_all/path_all/')
except:
error = True
# tries for a precise search for the GeneName, groups then by GeneName due to duplicate GeneNames
# with different RefSeq Names and Versions.
if searched_gene == '':
query = """
select g1.*, max(hvp_variantinstance.DateSubmitted) as DateSubmitted,
(select Count(hvp_variant.ID) as variants from hvp_variant
left join hvp_gene g2 on hvp_variant.Gene_id = g2.ID
where g2.GeneName = g1.GeneName) as Variants,
(select Count(hvp_variantinstance.ID) as variantInstances from hvp_variantinstance
left join hvp_variant on hvp_variantinstance.Variant_id = hvp_variant.ID
left join hvp_gene on hvp_variant.Gene_id = hvp_gene.ID
where hvp_gene.GeneName = g1.GeneName) as VariantInstances
from hvp_gene g1
left join hvp_variant on g1.ID = hvp_variant.Gene_id
left join hvp_variantinstance on hvp_variant.ID = hvp_variantinstance.Variant_id
group by GeneName
order by GeneName asc
"""
qs = Gene.objects.raw(query)
gene_list = list(qs)
else:
query = """
select g1.*, max(hvp_variantinstance.DateSubmitted) as DateSubmitted,
(select Count(hvp_variant.ID) as variants from hvp_variant
left join hvp_gene g2 on hvp_variant.Gene_id = g2.ID
where g2.GeneName = g1.GeneName) as Variants,
(select Count(hvp_variantinstance.ID) as variantInstances from hvp_variantinstance
left join hvp_variant on hvp_variantinstance.Variant_id = hvp_variant.ID
left join hvp_gene on hvp_variant.Gene_id = hvp_gene.ID
where hvp_gene.GeneName = g1.GeneName) as VariantInstances
from hvp_gene g1
left join hvp_variant on g1.ID = hvp_variant.Gene_id
left join hvp_variantinstance on hvp_variant.ID = hvp_variantinstance.Variant_id
where GeneName like %s
group by GeneName
order by GeneName asc
"""
qs = Gene.objects.raw(query, [searched_gene+'%'])
gene_list = list(qs)
# if nothing is return then we need to search in the other areas
if len(gene_list) == 0:
query = """
select g1.*, max(hvp_variantinstance.DateSubmitted) as DateSubmitted,
(select Count(hvp_variant.ID) as variants from hvp_variant
left join hvp_gene g2 on hvp_variant.Gene_id = g2.ID
where g2.GeneName = g1.GeneName) as Variants,
(select Count(hvp_variantinstance.ID) as variantInstances from hvp_variantinstance
left join hvp_variant on hvp_variantinstance.Variant_id = hvp_variant.ID
left join hvp_gene on hvp_variant.Gene_id = hvp_gene.ID
where hvp_gene.GeneName = g1.GeneName) as VariantInstances
from hvp_gene g1
left join hvp_variant on g1.ID = hvp_variant.Gene_id
left join hvp_variantinstance on hvp_variant.ID = hvp_variantinstance.Variant_id
where (RefSeqName like %s or GeneDescription like %s or HGNC_ID like %s
or AlternateSymbols like %s or AlternateNames like %s or Chromosome like %s
or PreviousSymbols like %s or PreviousNames like %s)
group by GeneName
order by GeneName asc
"""
qs = Gene.objects.raw(query, [searched_gene+'%', '%'+searched_gene+'%', searched_gene+'%', '%'+searched_gene+'%', '%'+searched_gene+'%', searched_gene+'%', '%'+searched_gene+'%', '%'+searched_gene+'%'])
gene_list = list(qs)
# if still nothing then look at the gene disease tags - using taggit
if len(gene_list) == 0:
# break down string into list
searched_gene_list = searched_gene.split(' ')
gene_list = Gene.objects.filter(DiseasesTags__name__in=searched_gene_list).distinct()
# number genes returned from search
gene_count = gene_list.count
# sets the paginator with the list of objects and number of objects per page
paginator = Paginator(gene_list, 10)
# gets the current page
page = request.GET.get('page')
try:
genes = paginator.page(page)
except PageNotAnInteger:
genes = paginator.page(1)
except EmptyPage:
genes = paginator.page(paginator.num_pages)
return render_to_response('search/gene_result.html',
{
'user': request.user,
'error': error,
'searched_gene': searched_gene,
'gene_count': gene_count,
'genes': genes,
'paginate_results': paginate_results,
},
context_instance=RequestContext(request))