Merge pull request #9 from UniOfLeicester/v0.0_series

V0.0 series

VERSION.txt

@@ -1 +1 @@
-0.1.0_dev_pre_a
+v0.2

VariantValidator/configuration/config.ini

@@ -1,6 +1,6 @@
 [variantValidator]
-version = 0.1.0_dev_pre_a
-release_date = tbc
+version = v0.2
+release_date = 2019-01-18
 
 [mysql]
 host = 127.0.0.1
@@ -9,8 +9,14 @@ user = vvadmin
 password = var1ant
 
 [logging]
-# string = error file console trace
-string = debug file console trace
+#Levels control verbosity and can be set to "critical" "error" "warning" "info" or "debug".
+level = info
+#level = debug
+console = true
+# Beware - file logging has permission issues.
+file = false
+# Trace is used for debugging to track variants through the validator function
+trace = false
 
 [EntrezID]
 entrezid = admin@variantvalidator.org

VariantValidator/testing/test_vv.py

@@ -44,6 +44,7 @@ def constructValidation(request):
 #    print request.param
     selectTranscripts='all'
     selectedAssembly='GRCh37'
+    os.environ["ADD_LOGS"]="True"
     return hub,hub.vv.validator(request.param,selectedAssembly,selectTranscripts)
 
 def test_validation_output(constructValidation):

VariantValidator/variantValidator.py

@@ -83,7 +83,7 @@
 import external
 import output_formatter
 import variantanalyser
-from vvLogging import logger
+from variantanalyser.vvLogging import logger
 from variantanalyser import functions as va_func
 from variantanalyser import dbControls as va_dbCrl
 from variantanalyser import hgvs2vcf as va_H2V
@@ -150,11 +150,20 @@ def loadConfigFile():
     if re.match('^\d+\.\d+\.\d+$', __version__) is not None:
         _is_released_version = True
     # Load database environments from config
-
-    logString = ConfigSectionMap("logging", Config)['string']
+    levelString = ConfigSectionMap("logging", Config)['level']
+    consoleString = ConfigSectionMap("logging", Config)['console']
+    if consoleString.lower()=="true":
+        consoleString="console"
+    fileString = ConfigSectionMap("logging", Config)['file']
+    if fileString.lower()=="true":
+        fileString="file"
+    traceString = ConfigSectionMap("logging", Config)['trace']
+    if traceString.lower()=="true":
+        traceString="trace"
+    logString = levelString+" "+consoleString+" "+fileString+" "+traceString
     os.environ["VALIDATOR_DEBUG"] = logString
-    print "ac", os.environ["VALIDATOR_DEBUG"]
-    print("ls", logString)
+    #print "ac", os.environ["VALIDATOR_DEBUG"]
+    #print("ls", logString)
 
 
 # Custom Exceptions
@@ -234,15 +243,10 @@ def my_config():
     hgvs_version = hgvs.__version__,
     hgvs_version = str(hgvs_version[0])
     locate = {
-        'seqrepo_directory': HGVS_SEQREPO_DIR,
-        'uta_url': UTA_DB_URL,
-        'py_liftover_directory': PYLIFTOVER_DIR,
-        'variantvalidator_data_url': VALIDATOR_DB_URL,
-        'entrez_id': ENTREZ_ID,
-        'variantvalidator_version': VERSION,
-        'variantvalidator_hgvs_version': hgvs_version,
-        'uta_schema': str(hdp.data_version()),
-        'seqrepo_db': HGVS_SEQREPO_DIR.split('/')[-1]
+        'variantvalidator_version': VERSION, #
+        'variantvalidator_hgvs_version': hgvs_version, #
+        'uta_schema': str(hdp.data_version()), #
+        'seqrepo_db': HGVS_SEQREPO_DIR.split('/')[-1] #
     }
     return locate
 
@@ -1117,7 +1121,10 @@ def validator(batch_variant, selected_assembly, select_transcripts, transcriptSe
                 except hgvs.exceptions.HGVSError as e:
                     error = str(e)
                 if error == 'false':
-                    input_parses.ac = input_parses.ac.upper()
+                    if 'LRG' in input_parses.ac:
+                        input_parses.ac.replace('T', 't')
+                    else:
+                        input_parses.ac = input_parses.ac.upper()
                     if hasattr(input_parses.posedit.edit, 'alt'):
                         if input_parses.posedit.edit.alt is not None:
                             input_parses.posedit.edit.alt = input_parses.posedit.edit.alt.upper()
@@ -1976,7 +1983,7 @@ def validator(batch_variant, selected_assembly, select_transcripts, transcriptSe
                         continue
                     else:
                         # Any transcripts?
-                        rel_var = va_func.relevant_transcripts(hgvs_mito, evm, hdp, alt_aln_method, reverse_normalizer)
+                        rel_var = va_func.relevant_transcripts(hgvs_mito, evm, hdp, alt_aln_method, reverse_normalizer, hp)
                         hgvs_genomic = copy.deepcopy(hgvs_mito)
                         if len(rel_var) == 0:
                             validation['genomic_g'] = valstr(hgvs_mito)
@@ -2257,7 +2264,7 @@ def validator(batch_variant, selected_assembly, select_transcripts, transcriptSe
                     Initial simple projection from the provided g. position all overlapping
                     transcripts
                     """
-                    rel_var = va_func.relevant_transcripts(hgvs_genomic, evm, hdp, alt_aln_method, reverse_normalizer)
+                    rel_var = va_func.relevant_transcripts(hgvs_genomic, evm, hdp, alt_aln_method, reverse_normalizer, hp)
 
                     # Double check rel_vars have not been missed when mapping from a RefSeqGene
                     if len(rel_var) != 0 and re.match('NG_', str(hgvs_genomic.ac)):
@@ -2270,7 +2277,7 @@ def validator(batch_variant, selected_assembly, select_transcripts, transcriptSe
                                 try_rel_var = []
                             else:
                                 try_rel_var = va_func.relevant_transcripts(hgvs_genomic, evm, hdp, alt_aln_method,
-                                                                           reverse_normalizer)
+                                                                           reverse_normalizer, hp)
                             if len(try_rel_var) > len(rel_var):
                                 rel_var = try_rel_var
                                 break
@@ -2285,7 +2292,7 @@ def validator(batch_variant, selected_assembly, select_transcripts, transcriptSe
                                  vcf_dict['alt']
                         hgvs_not_di = hp.parse_hgvs_variant(not_di)
                         rel_var = va_func.relevant_transcripts(hgvs_not_di, evm, hdp, alt_aln_method,
-                                                               reverse_normalizer)
+                                                               reverse_normalizer, hp)
 
                     # list return statements
                     """
@@ -8429,15 +8436,16 @@ def validator(batch_variant, selected_assembly, select_transcripts, transcriptSe
         logString = logger.getString()
         for l in logger.getString().split("\n"):
             logs.append(l)
-        metadata["logs"] = logString
-        metadata["variant"] = batch_variant
-        metadata["assembly"] = selected_assembly
-        metadata["transcripts"] = select_transcripts
-        metadata['seqrepo_directory'] = HGVS_SEQREPO_DIR
-        metadata['uta_url'] = UTA_DB_URL
-        metadata['py_liftover_directory'] = PYLIFTOVER_DIR
-        metadata['variantvalidator_data_url'] = VALIDATOR_DB_URL
-        metadata['entrez_id'] = ENTREZ_ID
+        if os.environ.get("ADD_LOGS")=="True":
+            metadata["logs"] = logString
+        #metadata["variant"] = batch_variant
+        #metadata["assembly"] = selected_assembly
+        #metadata["transcripts"] = select_transcripts
+        #metadata['seqrepo_directory'] = HGVS_SEQREPO_DIR
+        #metadata['uta_url'] = UTA_DB_URL
+        #metadata['py_liftover_directory'] = PYLIFTOVER_DIR
+        #metadata['variantvalidator_data_url'] = VALIDATOR_DB_URL
+        #metadata['entrez_id'] = ENTREZ_ID
         metadata['variantvalidator_version'] = VERSION
         metadata['variantvalidator_hgvs_version'] = hgvs_version
         metadata['uta_schema'] = str(hdp.data_version())
@@ -8689,7 +8697,7 @@ def hgvs2ref(query):
 
 def update_vv_data():
     import sys
-    logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
+    #logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
     # import update modules
     import mysql_refSeqGene_noMissmatch
     import compile_lrg_data

VariantValidator/variantanalyser/functions.py

@@ -2393,7 +2393,7 @@ def tx_exons(tx_ac, alt_ac, alt_aln_method, hdp):
 """
 
 
-def relevant_transcripts(hgvs_genomic, evm, hdp, alt_aln_method, reverse_normalizer):
+def relevant_transcripts(hgvs_genomic, evm, hdp, alt_aln_method, reverse_normalizer, hp):
     reverse_hn = reverse_normalizer
     # Pass relevant transcripts for the input variant to rts
     # Note, the evm method misses one end, the hdp. method misses the other. Combine both
@@ -2468,7 +2468,16 @@ def relevant_transcripts(hgvs_genomic, evm, hdp, alt_aln_method, reverse_normali
                 rev_hgvs_genomic = reverse_hn.normalize(hgvs_genomic)
                 # map back to coding
                 variant = evm.g_to_t(rev_hgvs_genomic, tx_ac)
-        code_var.append(str(variant))
+
+        strung = str(variant)
+        try:
+            hp.parse_hgvs_variant(strung)
+        except hgvs.exceptions.HGVSError:
+            continue
+        except TypeError:
+            continue
+        else:
+            code_var.append(str(variant))
     return code_var