Fixed VEP dash in deletions

kantale · Dec 7, 2016 · eb0cfd9 · eb0cfd9
1 parent d1fe9e9
commit eb0cfd9
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Showing 2 changed files with 28 additions and 2 deletions.
diff --git a/MutationInfo/__init__.py b/MutationInfo/__init__.py
@@ -2046,8 +2046,9 @@ def _search_VEP(self, variant, vep_assembly='grch38'):
 
  #In case of a deletion we need to make this correction in order to report the same position as in HGVS
  #For example: rs113993960 
- if variant_alleles == '':
+ if variant_alleles in [u'', u'-']:
  offset = v[0]['start']
+ variant_alleles = u'';
  else:
  offset = v[0]['end']
 

diff --git a/test/test.py b/test/test.py
@@ -8,6 +8,30 @@
 
 mi = MutationInfo()
 
+def remove_notes(r):
+ return {k:v for k,v in r.iteritems() if k != 'notes'}
+
+def which(program):
+ '''
+ Blatantly copied from http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python 
+ '''
+ import os
+ def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if is_exe(program):
+ return program
+ else:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ exe_file = os.path.join(path, program)
+ if is_exe(exe_file):
+ return exe_file
+
+ return None
+
 class TestMutationInfo(unittest.TestCase):
 
  maxDiff = None
@@ -85,6 +109,7 @@ def test_VARIATION_REPORTER(self):
  print ret
  self.assertEqual(ret, {'chrom': '7', 'notes': 'Variation Reporter converted NM_017781.2:c.166C>T to NC_000007.13:g.1023013C>T', 'source': 'NC_transcript', 'genome': 'GRCh37.p13', 'offset': 1023013, 'alt': 'T', 'ref': 'C'})
 
+ @unittest.skipIf(not which('transvar'), "transvar is not installed. Skipping..")
  def test_TRANSVAR(self):
  print '--------TRANSVAR------------------------'
 
@@ -168,7 +193,7 @@ def test_GET_INFO_HGVS(self):
 
  info = mi.get_info('NM_000367.2:c.-178C>T')
  print info
- self.assertEqual(info, {'chrom': '6', 'notes': '', 'source': 'counsyl_hgvs_to_vcf', 'genome': 'hg19', 'offset': 18155397, 'alt': 'A', 'ref': 'G'})
+ self.assertEqual(remove_notes(info), {'chrom': '6', 'source': 'counsyl_hgvs_to_vcf', 'genome': 'hg19', 'offset': 18155397, 'alt': 'A', 'ref': 'G'})
 
  info = mi.get_info('NT_005120.15:c.IVS1-72T>G', gene='UGT1A1')
  print info