def home(request):
# return variables
context = {}
errors = []
# form submission items
input_type = request.GET.get('input', '')
inputid = request.GET.get('inputid', '')
dnaseq = request.GET.get('dnaseq', '')
snplocation = request.GET.get('snplocation', '')
snpsubstitution = request.GET.get('snpsubstitution', '')
# search error checking
if request.GET:
if not input_type:
errors.append('Please select an input type')
elif input_type == 'dna':
dna_string = ""
for line in dnaseq:
dna_string += line.rstrip() # remove new line character from multiline DNA seq input
dnaseq = dna_string
valid_dna = re.match('^[ATCGatcg]*$', dnaseq, re.M)
if not dnaseq:
errors.append('Please enter a DNA sequence')
elif not valid_dna:
errors.append('Please enter a valid DNA sequence')
elif len(dnaseq) > 10000:
errors.append('Maximum DNA sequence input of 10,000 nucleotides')
else:
blast_ens_id, blast_snp_coordinate, blast_sub, blast_ancestral_snp, blast_snp_type, blast_snp_splice_site, blast_sift_prediction, blast_sift_score, blast_polyphen_prediction, blast_polyphen_score, blast_subjct_base, blast_query_base, blast_seq_before_snp, blast_seq_after_snp = seq_search(dnaseq)
context = dna_search(request, blast_ens_id, blast_snp_coordinate, blast_sub, blast_ancestral_snp, blast_snp_type, blast_snp_splice_site, blast_sift_prediction, blast_sift_score, blast_polyphen_prediction, blast_polyphen_score, blast_subjct_base, blast_query_base, blast_seq_before_snp, blast_seq_after_snp)
connection.close()
return render(request, 'snippy/dna_results.html', context)
elif not inputid and not dnaseq and not snplocation and not snpsubstitution:
errors.append('Please enter a search term')
elif input_type == 'rsid':
if not inputid:
errors.append('Please enter an rsID')
elif not Variation.objects.filter(name=inputid).exists():
errors.append('Please enter a valid rsID')
# rsID search
elif inputid:
context = rs_search(request)
connection.close()
return render(request, 'snippy/rs_results.html', context)
elif input_type == 'ensemblid':
if not inputid:
errors.append('Please enter an Ensembl gene ID')
elif not Gene.objects.filter(stable_id=inputid).exists():
errors.append('Please enter a valid Ensembl gene ID')
# ensembl ID search
elif inputid:
if not snplocation:
errors.append('Please enter a SNP location')
elif snplocation.isdigit() is False:
if ':' and '.' not in snplocation:
errors.append('Please enter a SNP location in the format 24193 or 13:g.32339667')
elif SeqRegion.objects.filter(name=snplocation.split(':')[0]).exists() and snplocation.split('.')[1].isdigit():
context = ensembl_search(request)
connection.close()
return render(request, 'snippy/ensembl_results.html', context)
elif snplocation.isdigit() == True:
context = ensembl_search(request)
connection.close()
return render(request, 'snippy/ensembl_results.html', context)
# return errors
else:
connection.close()
return render(request, 'snippy/home.html', {'errors': errors})
# return home as standard
connection.close()
return render(request, 'snippy/home.html', {'errors': errors})
def test_seq_search():
alist = range(10)
random.shuffle(alist)
assert search.seq_search(alist, 5)
assert not search.seq_search(alist, 11)
