Merge pull request #483 from mutalyzer/fix-482

Update HGVS descriptions retrieval for SNP converter (#482)

.travis.yml

 # Validate this file using http://lint.travis-ci.org/
+dist: xenial
 language: python
 sudo: false
 cache: pip
@@ -6,7 +7,9 @@ python: "2.7"
 addons:
   apt_packages: swig
   postgresql: "9.4"
-services: redis-server
+services:
+  - redis-server
+  - mysql
 before_install:
   - CFLAGS=-O0 pip install -r requirements.txt
   - pip install psycopg2

mutalyzer/ncbi.py

@@ -394,7 +394,7 @@ def rsid_to_descriptions(rsid, output):
     try:
         # Parse the output.
         doc = minidom.parseString(response_text)
-        rs = doc.getElementsByTagName('Rs')[0]
+        docsum = doc.getElementsByTagName('DOCSUM')[0].childNodes[0].data
     except expat.ExpatError:
         # TODO: Log error.
         raise ServiceError()
@@ -402,7 +402,11 @@ def rsid_to_descriptions(rsid, output):
         # The expected root element is not present, this has also been
         # observed as a response for non-existing rs#.
         output.addMessage(__file__, 2, 'EENTREZ',
-                          'Non existing %s in the DB or no root element.' % rsid)
+                          'Non existing %s in the DB or no root element.'
+                          % rsid)
         return []
 
-    return [hgvs.lastChild.data for hgvs in rs.getElementsByTagName('hgvs')]
+    for part in docsum.split('|'):
+        if part.startswith('HGVS='):
+            return part.split('=')[1].split(',')
+    return []

tests/test_scheduler.py

@@ -76,18 +76,17 @@ def test_snp_converter():
     """
     snps = ['rs9919552']
     expected = [['rs9919552',
-                 '|'.join(['NC_000011.9:g.111959625C>T',
-                           'NG_012337.2:g.7055C>T',
-                           'NG_033145.1:g.2898G>A',
-                           'NM_001276503.1:c.169+928C>T',
-                           'NM_001276504.1:c.87C>T',
-                           'NM_001276506.1:c.204C>T',
+                 '|'.join(['NC_000011.10:g.112088901C>T',
+                           'NC_000011.9:g.111959625C>T',
+                           'NG_012337.3:g.7055C>T',
+                           'NM_003002.4:c.204C>T',
                            'NM_003002.3:c.204C>T',
-                           'NP_001263433.1:p.Ser29=',
-                           'NP_001263435.1:p.Ser68=',
-                           'NP_002993.1:p.Ser68=',
+                           'NM_001276506.2:c.204C>T',
+                           'NM_001276506.1:c.204C>T',
+                           'NM_001276504.2:c.87C>T',
+                           'NM_001276504.1:c.87C>T',
                            'NR_077060.1:n.288C>T',
-                           'NT_033899.8:g.15522041C>T'])]]
+                           'NG_033145.1:g.2898G>A'])]]
 
     # Patch Bio.Entrez.efetch to return dbSNP record for rs9919552.
     def mock_efetch(*args, **kwargs):

tests/test_services_soap.py

@@ -445,9 +445,8 @@ def test_getdbsnpdescriptions(api):
         r = api('getdbSNPDescriptions', 'rs9919552')
 
     assert 'NC_000011.9:g.111959625C>T' in r.string
-    assert 'NG_012337.2:g.7055C>T' in r.string
+    assert 'NG_012337.3:g.7055C>T' in r.string
     assert 'NM_003002.3:c.204C>T' in r.string
-    assert 'NP_002993.1:p.Ser68=' in r.string
 
 
 @pytest.mark.usefixtures('hg19_transcript_mappings')

tests/test_website.py

@@ -364,9 +364,8 @@ def test_snp_converter_valid(website):
     assert '0 Errors' in r.data
     assert '0 Warnings' in r.data
     assert 'NC_000011.9:g.111959625C>T' in r.data
-    assert 'NG_012337.2:g.7055C>T' in r.data
+    assert 'NG_012337.3:g.7055C>T' in r.data
     assert 'NM_003002.3:c.204C>T' in r.data
-    assert 'NP_002993.1:p.Ser68=' in r.data
 
 
 def test_snp_converter_invalid(website):