def gene_snps_filter(request):
flanks = int(request.GET.get('f'))
order_by = request.GET.get('order_by', 'library__library_code')
gene = request.GET.get('s')
fmin = Feature.objects.values_list(
'fmin', flat=True).filter(geneid=gene).filter(featuretype='gene')[0]
fmax = Feature.objects.values_list(
'fmax', flat=True).filter(geneid=gene).filter(featuretype='gene')[0]
try:
cds_fmin = Feature.objects.values_list('fmin', flat=True).filter(
geneid=gene, featuretype='CDS')[0]
cds_fmax = Feature.objects.values_list('fmax', flat=True).filter(
geneid=gene, featuretype='CDS')[0]
except IndexError:
print "There are no CDS regions associated with this gene."
cds_fmin = 0
cds_fmax = 0
pass
result_list = SNP.objects.values(
'library__library_code', 'result_id', 'chromosome__chromosome_name',
'snp_id', 'snp_position', 'ref_base', 'alt_base').filter(
snp_position__range=(
(Feature.objects.values_list('fmin', flat=True).filter(
geneid=gene).filter(featuretype='gene')[0]) + flanks,
(Feature.objects.values_list('fmax', flat=True).filter(
geneid=gene).filter(featuretype='gene')[0]) + flanks),
chromosome__chromosome_name=Feature.objects.values_list(
'chromosome', flat=True).filter(geneid=gene).filter(
featuretype='gene')[0]).order_by(order_by)
count = result_list.count()
paginator = Paginator(result_list, 50)
page = request.GET.get('page')
filter_urls = build_orderby_urls(request.get_full_path(), [
'library__library_code', 'result_id', 'chromosome__chromosome_name',
'snp_id', 'snp_position', 'ref_base', 'alt_base'
])
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response(
'snpdb/snps_in_gene_filter.html', {
"results": results,
"filter_urls": filter_urls,
"paginator": paginator,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min,
"cds_fmin": cds_fmin,
"cds_fmax": cds_fmax,
"fmin": fmin,
"fmax": fmax,
"gene": gene,
"count": count
})
def gene_list(request):
order_by = request.GET.get('order_by', 'start')
library = request.GET.get('lib')
results = Feature.objects.values(
'geneid', 'fmin', 'fmax', 'chromosome').filter(
featuretype='gene',
genome__organism__library__library_code=library).order_by(order_by)
count = len(results)
paginator = Paginator(results, 200)
page = request.GET.get('page')
filter_urls = build_orderby_urls(request.get_full_path(),
['geneid', 'chromosome', 'fmin', 'fmax'])
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response(
'snpdb/gene_list.html', {
"results": results,
"library": library,
"count": count,
"filter_urls": filter_urls,
"paginator": paginator,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
})
def gene_feature(request):
geneid = request.GET.get('geneid')
order_by = request.GET.get('order_by', 'geneid')
feature = Feature.objects.all().filter(
geneid=geneid, featuretype='gene').order_by(order_by)
paginator = Paginator(feature, 50)
page = request.GET.get('page')
filter_urls = build_orderby_urls(request.get_full_path(), [
'snp_id', 'snp_position', 'ref_base', 'alt_base',
'library__library_code'
])
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response(
'snpdb/gene_feature.html', {
"geneid": geneid,
"results": results,
"filter_urls": filter_urls,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min,
})
def library_snp_summary(request):
order_by = request.GET.get('order_by', 'library')
results = SNP.objects.values(
'library_id',
'library__library_code',
'result__genome__organism__organismcode',
).distinct().annotate(
num_snps=Count('snp_id'),
hetero=BooleanSum('heterozygosity'),
indel=BooleanSum('snp_type__indel'),
trans=BooleanSum('snp_type__transition'),
).order_by(order_by)
result = []
for each in results:
library = each['library__library_code']
organismcode = SNP.objects.values_list(
'result__genome__organism__organismcode',
flat=True).filter(library__library_code=library)[0]
contig = get_chromosome_size(organismcode)
for key, value in contig.iteritems():
each[key] = value
result.append(each)
paginator = Paginator(result, 50)
page = request.GET.get('page')
count = len(result)
# Calls utils method to append new filters or order_by to the current url
filter_urls = build_orderby_urls(request.get_full_path(), [
'library__library_id', 'library__library_code', 'snp_id', 'num_snps',
'hetero', 'h**o', 'indel', 'trans', 'snp_density'
])
try:
result = paginator.page(page)
except PageNotAnInteger:
result = paginator.page(1)
except EmptyPage:
result = paginator.page(paginator.num_pages)
toolbar_max = min(result.number + 4, paginator.num_pages)
toolbar_min = max(result.number - 4, 0)
return render_to_response(
'snpdb/library_snp_summary.html', {
"result": result,
"count": count,
"filter_urls": filter_urls,
"paginator": paginator,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
})
def compare_gene_lib(request):
order_by = request.GET.get('order_by', 'library__library_code')
gene = request.GET.get('s')
if not gene:
return render_to_response('snpdb/compare_gene_library.html')
else:
genes = gene.split()
genomes = Feature.objects.values_list(
'genome_id', flat=True).filter(geneid__in=genes).distinct()
libraries = []
for each in genomes:
result_list = SNP.objects.values(
'library__library_code',
'result__genome__organism__organismcode',
'result__genome__version', 'result__genome__genome_id').filter(
result__genome__genome_id=each).distinct().order_by(
order_by)
libraries.append(result_list)
page = request.GET.get('page')
filter_urls = build_orderby_urls(request.get_full_path(), [
'library__library_code', 'result__genome__organism__organismcode',
'result__genome____genome_id', 'result__genome__version'
])
count = len(libraries)
paginator = Paginator(libraries, 50)
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response(
'snpdb/compare_gene_library_filter.html', {
"results": results,
"gene": gene,
"count": count,
"filter_urls": filter_urls,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
})
def chromosome_library_snp_summary_filter(request):
order_by = request.GET.get('order_by', 'chromosome__chromosome_name')
library = request.GET.get('library')
results = SNP.objects.values(
'chromosome__chromosome_name', 'library_id', 'library__library_code',
'result__genome__organism__organismcode').filter(
library__library_code=library).annotate(
num_snps=Count('snp_id'),
hetero=BooleanSum('heterozygosity'),
indel=BooleanSum('snp_type__indel'),
trans=BooleanSum('snp_type__transition'))
organismcode = SNP.objects.values_list(
'result__genome__organism__organismcode',
flat=True).filter(library__library_code=library)[0]
library_size = get_chromosome_size(organismcode)
result_list = results.order_by(order_by)
paginator = Paginator(result_list, 50)
page = request.GET.get('page')
# Calls utils method to append new filters or order_by to the current url
filter_urls = build_orderby_urls(request.get_full_path(), [
'chromosome__chromosome_name', 'library__librarysize', 'library_id',
'library__library_code', 'num_snps', 'hetero', 'trans', 'indel'
])
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response(
'snpdb/chromosome_library_snp_summary_filter.html', {
"results": results,
"library_size": library_size,
"filter_urls": filter_urls,
"paginator": paginator,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
})
def impact_snps(request):
# Collects all values from the GET request
analysis_path = request.GET.get('analysis_path')
group1 = ast.literal_eval(request.GET.get('add'))
group2 = ast.literal_eval(request.GET.get('neg'))
wt = request.GET.get('wt')
libraries = group1 + group2
impact = request.GET.get('impact')
order_by = request.GET.get('order_by', 'chromosome')
s = request.GET.get('s')
att = request.GET.get('att')
high_ct = request.GET.get('high_ct')
moderate_ct = request.GET.get('moderate_ct')
low_ct = request.GET.get('low_ct')
group1.sort()
group2.sort()
result_path_0 = os.path.join(analysis_path, '0000.vcf')
result_path_1 = os.path.join(analysis_path, '0001.vcf')
output_path_0 = os.path.join(analysis_path, '%s_impact_0000.vcf' % impact)
output_path_1 = os.path.join(analysis_path, '%s_impact_0001.vcf' % impact)
print settings.MEDIA_URL
java_jar = settings.SNPEFF_JAR_PATH
print java_jar
#If output file has not been created
if not os.path.isfile(output_path_1):
#If no specific sort is required
if not s:
cmd = """cat %s| java -jar %s "( ANN[*].IMPACT = '%s')" > %s """
subprocess.call(cmd %
(result_path_0, java_jar, impact, output_path_0),
shell=True,
stdout=subprocess.PIPE)
subprocess.call(cmd %
(result_path_1, java_jar, impact, output_path_1),
shell=True,
stdout=subprocess.PIPE)
#Sorts results by specified value
else:
print "In else statement"
if att == "0":
s = int(s)
cmd = """cat %s | /usr/local/snpEff/scripts/vcfEffOnePerLine.pl | java -jar %s "(ANN[*].IMPACT = '%s') & (POS = %d)" """
elif att == "ref":
cmd = """cat %s | /usr/local/snpEff/scripts/vcfEffOnePerLine.pl | java -jar %s "(ANN[*].IMPACT = '%s') & (REF = '%s')" """
elif att == "alt":
cmd = """cat %s | /usr/local/snpEff/scripts/vcfEffOnePerLine.pl | java -jar %s "(ANN[*].IMPACT = '%s') & (ALT = '%s')" """
elif att == "quality":
s = int(s)
cmd = """cat %s | /usr/local/snpEff/scripts/vcfEffOnePerLine.pl | java -jar %s "(ANN[*].IMPACT = '%s') & (QUAL = %d)" """
elif att == "chromosome":
cmd = """cat %s | /usr/local/snpEff/scripts/vcfEffOnePerLine.pl | java -jar %s "(ANN[*].IMPACT = '%s') & (CHROM =~ '%s')" """
elif att == "impact":
s = s.replace(' ', '_').upper()
cmd = """cat %s | /usr/local/snpEff/scripts/vcfEffOnePerLine.pl | java -jar %s "(ANN[*].IMPACT = '%s') & (ANN[*].EFFECT = '%s')" """
elif att == "gene":
cmd = """cat %s | /usr/local/snpEff/scripts/vcfEffOnePerLine.pl | java -jar %s "(ANN[*].IMPACT = '%s') & (ANN[*].GENE = '%s')" """
subprocess.call(
cmd % (result_path_0, java_jar, impact, output_path_0, s),
shell=True,
stdout=subprocess.PIPE)
subprocess.call(
cmd % (result_path_1, java_jar, impact, output_path_1, s),
shell=True,
stdout=subprocess.PIPE)
snp_dict = defaultdict(dict)
snp_dicts = add_snps_from_vcf(output_path_0, libraries, group1, snp_dict,
wt, impact)
snp_dicts = add_snps_from_vcf(output_path_1, libraries, group2,
snp_dicts[0], wt, impact)
genome_id = snp_dicts[1]
test_dict = dict(snp_dict)
if order_by == '0':
sorted_snp = sorted(test_dict.iteritems())
elif order_by == 'quality':
sorted_snp = sorted(test_dict.iteritems(),
key=lambda (k, d): (
d['chromosome'],
k,
))
else:
sorted_snp = sorted(test_dict.iteritems(),
key=lambda (k, d): (
d['chromosome'],
k,
))
count = len(snp_dict)
paginator = Paginator(sorted_snp, 200)
page = request.GET.get('page')
# Calls utils method to append new filters or order_by to the current url
filter_urls = build_orderby_urls(request.get_full_path(), [
'chromosome', 'ref', 'quality', 'impact', 'gene', 'gene_length', 'aa',
'wt_allele', 'alt', 'group1_consistency', 'group2_consistency'
])
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
c = {
"analysis_path": analysis_path,
"paginator": paginator,
"results": results,
"libraries": libraries,
"add": group1,
"impact": impact,
"neg": group2,
"wt": wt,
"high_ct": high_ct,
"low_ct": low_ct,
"moderate_ct": moderate_ct,
"filter_urls": filter_urls,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min,
"count": count,
"genome_id": genome_id
}
return render_to_response('snpdb/impact_snps_search.html',
c,
context_instance=RequestContext(request))
def library_gene_snps_filter(request):
order_by = request.GET.get('order_by', 'library__library_code')
gene = request.GET.get('s')
library = request.GET.get('lib')
cds_fmin = Feature.objects.values_list('fmin', flat=True).filter(
geneid=gene, featuretype='CDS')[0]
cds_fmax = Feature.objects.values_list('fmax', flat=True).filter(
geneid=gene, featuretype='CDS')[0]
fmin = Feature.objects.values_list(
'fmin', flat=True).filter(geneid=gene).filter(featuretype='gene')[0]
fmax = Feature.objects.values_list(
'fmax', flat=True).filter(geneid=gene).filter(featuretype='gene')[0]
result_list = SNP.objects.values(
'library__library_code', 'result_id', 'chromosome__chromosome_name',
'snp_id', 'snp_position', 'ref_base', 'alt_base', 'quality',
'heterozygosity').filter(
snp_position__range=(Feature.objects.values_list(
'fmin',
flat=True).filter(geneid=gene).filter(featuretype='gene')[0],
Feature.objects.values_list(
'fmax',
flat=True).filter(geneid=gene).filter(
featuretype='gene')[0]),
library__library_code=library,
chromosome__chromosome_name=Feature.objects.values_list(
'chromosome', flat=True).filter(geneid=gene).filter(
featuretype='gene')[0]).order_by(order_by)
count = result_list.count()
page = request.GET.get('page')
filter_urls = build_orderby_urls(request.get_full_path(), [
'library__library_code', 'result_id', 'chromosome__chromosome_name',
'snp_id', 'snp_position', 'ref_base', 'alt_base', 'quality',
'heterozygosity'
])
paginator = Paginator(result_list, 50)
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
print "Error"
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
print toolbar_max
return render_to_response(
'snpdb/library_to_snp_filter.html', {
"results": results,
"gene": gene,
"library": library,
"cds_fmin": cds_fmin,
"cds_fmax": cds_fmax,
"fmin": fmin,
"fmax": fmax,
"filter_urls": filter_urls,
"paginator": paginator,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min,
"count": count
})
def compare_gene_lib_filter_results(request):
order_by = request.GET.get('order_by', 'library__library_code')
gene = request.GET.get('s')
library = request.GET.getlist('check')
#Gets the start and stop position of the coding region of the gene.
cds_fmin = Feature.objects.values_list('fmin', flat=True).filter(
geneid=gene, featuretype='CDS')[0]
cds_fmax = Feature.objects.values_list('fmax', flat=True).filter(
geneid=gene, featuretype='CDS')[0]
#Gets the start and stop position of gene.
fmin = Feature.objects.filter(geneid=gene).filter(
featuretype='gene').values('fmin')[0]
fmax = Feature.objects.filter(geneid=gene).filter(
featuretype='gene').values('fmax')[0]
#Collects libraries that are effected by this gene
result_list = SNP.objects.values(
'snp_id', 'snp_position', 'ref_base', 'alt_base',
'library__library_code').filter(
library__library_code__in=library,
snp_position__range=(Feature.objects.values_list(
'fmin',
flat=True).filter(geneid=gene).filter(featuretype='gene')[0],
Feature.objects.values_list(
'fmax',
flat=True).filter(geneid=gene).filter(
featuretype='gene')[0]),
chromosome__chromosome_name=Feature.objects.values_list(
'chromosome', flat=True).filter(geneid=gene).filter(
featuretype='gene')[0]).order_by(order_by)
snp_group = []
library_group = []
max_snps = 0
count = 0
for each in result_list:
snp_position = each['snp_position']
library = each['library__library_code']
if snp_position in snp_group:
count += 1
pass
else:
snp_group.append(snp_position)
count = 1
pass
if count > max_snps:
max_snps = count
count = 0
if library in library_group:
pass
else:
library_group.append(library)
paginator = Paginator(result_list, 50)
page = request.GET.get('page')
filter_urls = build_orderby_urls(request.get_full_path(), [
'snp_id', 'snp_position', 'ref_base', 'alt_base',
'library__library_code'
])
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response(
'snpdb/compare_gene_library_filter_result.html', {
"results": results,
"gene": gene,
"cds_fmin": cds_fmin,
"cds_fmax": cds_fmax,
"fmin": fmin,
"fmax": fmax,
"count": len(snp_group),
"library_group": library_group,
"snp_group": snp_group,
"max_snps": range(max_snps),
"filter_urls": filter_urls,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
})
def compare_gene_lib_results(request):
# order_by = request.GET.get('order_by', 'library__library_code')
gene_string = request.GET.get('s')
genes = gene_string.split()
library_data = request.GET.getlist('check')
library = []
genome_id = []
for each in library_data:
data = each.split('_')
library.append(data[0])
if data[1] not in genome_id:
genome_id.append(data[1])
test = {}
for gene in genes:
try:
cds_fmin = Feature.objects.values_list('fmin', flat=True).filter(
geneid=gene, genome_id__in=genome_id, featuretype='CDS')[0]
cds_fmax = Feature.objects.values_list('fmax', flat=True).filter(
geneid=gene, genome_id__in=genome_id, featuretype='CDS')[0]
except IndexError:
cds_fmin = 0
cds_fmax = 0
try:
fmin = Feature.objects.filter(
geneid=gene, genome_id__in=genome_id).filter(
featuretype='gene').values('fmin')[0]
fmax = Feature.objects.filter(
geneid=gene, genome_id__in=genome_id).filter(
featuretype='gene').values('fmax')[0]
except IndexError:
fmin = 0
fmax = 0
chromosome = Feature.objects.filter(
geneid=gene,
genome_id__in=genome_id).filter(featuretype='gene').values_list(
'chromosome', flat=True)[0]
result_list = SNP.objects.filter(
effect__effect_id=6,
effect__effect_string__exact=gene,
library__library_code__in=library).values(
'library', 'library__library_code', 'snp_id', 'snp_position',
'ref_base', 'alt_base', 'heterozygosity', 'quality',
'chromosome__chromosome_name', 'effect__effect_string',
'effect__effect_class',
'effect__effect').distinct().order_by('snp_position')
#Checks to see if tuples have all libraries present. Inserts blank tuples if not.
for each in result_list:
new_tuple = [
(None, None, None, gene, cds_fmin, cds_fmax, fmin['fmin'],
fmax['fmax'], chromosome, each['snp_position'])
] * len(library)
curr_library = each['library__library_code']
tup = (curr_library, each['ref_base'], each['alt_base'], gene,
cds_fmin, cds_fmax, fmin['fmin'], fmax['fmax'], chromosome,
each['snp_position'])
index = library.index(curr_library)
if each['snp_position'] in test:
current_tup = test[each['snp_position']]
current_tup[index] = tup
test[each['snp_position']] = current_tup
else:
new_tuple[index] = tup
test[each['snp_position']] = new_tuple
test = OrderedDict(sorted(test.items(), key=lambda key: key[0]))
count = len(test)
filter_urls = build_orderby_urls(request.get_full_path(), [
'gene', 'snp_position', 'ref_base', 'alt_base',
'library__library_code', 'fmin', 'fmax'
])
paginator = Paginator(test.items(), 50)
page = request.GET.get('page')
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response('snpdb/compare_gene_library_filter_result.html',
{
"results": results,
"genes": genes,
"gene": gene_string,
"library": library,
"test": test,
"count": count,
"library_group": sorted(library),
"filter_urls": filter_urls,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
},
context_instance=RequestContext(request))
def compare_cnv_libraries(request):
ref_genome = request.GET.get('ref_genome')
library_codes = request.GET.getlist('library_codes')
chromosome = request.GET.getlist('chromosome')
order_by = request.GET.get('order_by', 'start').encode('UTF8')
if chromosome and library_codes:
result_list = CNV.objects.values(
'start', 'stop', 'library__library_code', 'coverage',
'cnv_value').filter(library__library_code__in=library_codes,
cnv_type=1,
chromosome__chromosome_name=chromosome[0])
somy_list = CNV.objects.values(
'library__library_code',
'cnv_value').filter(library__library_code__in=library_codes,
cnv_type=2,
chromosome__chromosome_name=chromosome[0])
somys = {}
for each in somy_list:
if each['library__library_code'].encode('UTF8') not in somys:
somys[each['library__library_code'].encode(
'UTF8')] = each['cnv_value']
cnv_dict = {}
#Checks to see if tuples have all libraries present. Inserts blank tuples if not.
for each in result_list:
pos = chromosome[0] + '_' + str(each['start'])
if pos in cnv_dict:
library_dict = {
'cnv': each['cnv_value'],
'coverage': each['coverage'],
'somy': somys[each['library__library_code'].encode('UTF8')]
}
if each['library__library_code'] not in cnv_dict[pos]:
cnv_dict[pos][each['library__library_code'].encode(
'UTF8')] = library_dict
else:
library_dict = {
each['library__library_code'].encode('UTF8'): {
'cnv': each['cnv_value'],
'coverage': each['coverage'],
'somy':
somys[each['library__library_code'].encode('UTF8')]
},
'start': each['start'],
'stop': each['stop']
}
cnv_dict[pos] = library_dict
cnvs = cnv_dict.items()
if order_by == 'cnv':
lib = request.GET.get('lib').encode('UTF8')
cnvs.sort(key=lambda (k, d): (
d[lib],
d['start'],
))
else:
cnvs.sort(key=lambda (k, d): (
d[order_by],
d['start'],
))
# Calls utils method to append new filters or order_by to the current url
filter_urls = build_orderby_urls(request.get_full_path(), [
'chromosome', 'start', 'stop', 'cnv', 'coverage', 'library', 'somy'
])
paginator = Paginator(cnvs, 50)
page = request.GET.get('page')
try:
cnvs = paginator.page(page)
except PageNotAnInteger:
cnvs = paginator.page(1)
except EmptyPage:
cnvs = paginator.page(paginator.num_pages)
toolbar_max = min(cnvs.number + 4, paginator.num_pages)
toolbar_min = max(cnvs.number - 4, 0)
return render_to_response('snpdb/compare_cnv_libraries.html', {
"cnvs": cnvs,
"somys": somys,
"chromosome": chromosome[0],
"ref_genome": ref_genome,
"library_codes": library_codes,
"filter_urls": filter_urls,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
},
context_instance=RequestContext(request))
elif library_codes and not chromosome:
print library_codes, type(library_codes)
chrom_list = Chromosome.objects.values('chromosome_name').filter(
genome_name=ref_genome).order_by('chromosome_name')
page = request.GET.get('page')
paginator = Paginator(chrom_list, 500)
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response('snpdb/compare_cnv_libraries.html', {
"results": results,
"library_codes": library_codes,
"paginator": paginator,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
},
context_instance=RequestContext(request))
elif ref_genome:
lib_list = Library.objects.values(
'library_code', 'result__genome__organism__organismcode').filter(
result__genome__organism__organismcode=ref_genome).distinct(
).order_by('library_code')
else:
lib_list = Organism.objects.values('organismcode').distinct().order_by(
'organismcode')
page = request.GET.get('page')
paginator = Paginator(lib_list, 500)
try:
results = paginator.page(page)
except PageNotAnInteger:
results = paginator.page(1)
except EmptyPage:
results = paginator.page(paginator.num_pages)
toolbar_max = min(results.number + 4, paginator.num_pages)
toolbar_min = max(results.number - 4, 0)
return render_to_response('snpdb/compare_cnv_libraries.html', {
"results": results,
"ref_genome": ref_genome,
"paginator": paginator,
"toolbar_max": toolbar_max,
"toolbar_min": toolbar_min
},
context_instance=RequestContext(request))
