def test_FYZZY_HGVS_CORRECTOR(self):
print '------FUZZY HGVS CORRECTOR---------'
ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C')
print ret
self.assertEqual(ret, None)
ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1')
print ret
self.assertEqual(ret, None)
try:
MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1', ref_type='p')
except Exception as e:
self.assertEqual(str(e), 'Available values for ref_type: None, "c" and "g" . Found: p')
ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1', ref_type='c')
print ret
self.assertEqual(ret, 'NM_001042351.1:c.1048G>C')
ret = MutationInfo.fuzzy_hgvs_corrector('1387C->T/A', transcript='NM_001042351.1', ref_type='c')
print ret
self.assertEqual(ret, ['NM_001042351.1:c.1387C>T', 'NM_001042351.1:c.1387C>A'])
ret = MutationInfo.fuzzy_hgvs_corrector('1387C->T/A')
print ret
self.assertEqual(ret, None)
ret = MutationInfo.fuzzy_hgvs_corrector('-1923(A>C)', transcript='NT_005120.15', ref_type='g')
print ret
self.assertEqual(ret, 'NT_005120.15:g.-1923A>C')
ret = MutationInfo.fuzzy_hgvs_corrector('NT_005120.15:c.1160(CC>GT)')
print ret
self.assertEqual(ret, 'NT_005120.15:c.1160_1161delinsGT')
def test_FYZZY_HGVS_CORRECTOR(self):
print '------FUZZY HGVS CORRECTOR---------'
ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C')
print ret
self.assertEqual(ret, None)
ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C',
transcript='NM_001042351.1')
print ret
self.assertEqual(ret, None)
try:
MutationInfo.fuzzy_hgvs_corrector('1048G->C',
transcript='NM_001042351.1',
ref_type='p')
except Exception as e:
self.assertEqual(
str(e),
'Available values for ref_type: None, "c" and "g" . Found: p')
ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C',
transcript='NM_001042351.1',
ref_type='c')
print ret
self.assertEqual(ret, 'NM_001042351.1:c.1048G>C')
ret = MutationInfo.fuzzy_hgvs_corrector('1387C->T/A',
transcript='NM_001042351.1',
ref_type='c')
print ret
self.assertEqual(
ret, ['NM_001042351.1:c.1387C>T', 'NM_001042351.1:c.1387C>A'])
ret = MutationInfo.fuzzy_hgvs_corrector('1387C->T/A')
print ret
self.assertEqual(ret, None)
ret = MutationInfo.fuzzy_hgvs_corrector('-1923(A>C)',
transcript='NT_005120.15',
ref_type='g')
print ret
self.assertEqual(ret, 'NT_005120.15:g.-1923A>C')
ret = MutationInfo.fuzzy_hgvs_corrector('NT_005120.15:c.1160(CC>GT)')
print ret
self.assertEqual(ret, 'NT_005120.15:c.1160_1161delinsGT')
from django.shortcuts import render
from django.http import HttpResponse
import json
import uuid
import logging
import StringIO
from pyVEP import VEP
from MutationInfo import MutationInfo
print 'Initializing MutationInfo..'
mi = MutationInfo()
print 'Done'
root_logger = logging.getLogger()
root_logger.setLevel(logging.DEBUG)
# Create your views here.
def do_MutationInfo(request):
'''
test_ret = {'chrom': '12', 'source': 'NC_transcript', 'genome': 'GRCh37.p13', 'offset': 21355487, 'alt': 'G', 'ref': 'T'}
'''
print request.method
if request.method == u'GET':
def test_HGVS_PARSER(self):
print '--------HGVS PARSER-----------------'
ret = MutationInfo.biocommons_parse('unparsable')
print ret
self.assertEqual(ret, None)
def test_HGVS_PARSER(self):
print '--------HGVS PARSER-----------------'
ret = MutationInfo.biocommons_parse('unparsable')
print ret
self.assertEqual(ret, None)
