Merge branch 'master' of https://gitlab.isb-sib.ch/bgao/arraymapVariant-callsMapping

merge

arraymap2ga4gh.py

@@ -66,6 +66,7 @@ def cli(input_db, input_collection, output_db, output_collection_individuals, ou
     callsets = {}
     variants = {}
     variantset_id = 'AM_VS_HG18'
+
     # counter for demo mode
     sampleno = 1
 
@@ -88,9 +89,6 @@ def cli(input_db, input_collection, output_db, output_collection_individuals, ou
     varid = 1
     callno = 0
 
-
-
-
     ########################################
     # return the number of processed samples
     ########################################
@@ -205,9 +203,9 @@ def cli(input_db, input_collection, output_db, output_collection_individuals, ou
             ###########################################################
 
             #only samples with enough attributes are assumed to be valid, the threshold is set to 50 arbitrarily.
-            # MODI: reduce threshold to 25
+            # MODI: reduce threshold to 30
             # TODO: check & discuss => ?!
-            if (len(sample) > 25):
+            if (len(sample) > 30):
                 no_validSamples += 1
 
                 # generate ids
@@ -246,6 +244,21 @@ def cli(input_db, input_collection, output_db, output_collection_individuals, ou
                     # TODO: fixing country names should be in an external cleanup script
                     country = string.capwords(get_attribute('COUNTRY', sample))
                     country = re.sub('USA', 'United States', country, flags=re.IGNORECASE)
+                    countryMatchObj = re.search('\w', country)
+
+                    city = string.capwords(get_attribute('CITY', sample))
+                    cityMatchObj = re.search('\w', city)
+
+                    geoLabel = ''
+                    geoPrecision = ''
+                    if cityMatchObj:
+                        geoLabel = city
+                        geoPrecision = 'city'
+                        if countryMatchObj:
+                            geoLabel = geoLabel+', '+country
+                    elif countryMatchObj:
+                        geoLabel = country
+                        geoPrecision = 'country'
 
 
                     biosamples[biosample_id] = {
@@ -285,13 +298,9 @@ def cli(input_db, input_collection, output_db, output_collection_individuals, ou
                                                 'individual_id': individual_id,
                                                 'individual_age_at_collection': get_attribute('AGEISO', sample),
                                                 'external_identifiers': external_ids,
+                                                'location': { 'geo_label': geoLabel,  'geo_precision': geoPrecision, 'latitude': get_attribute('GEOLAT', sample, 'float', ''), 'longitude': get_attribute('GEOLONG', sample, 'float', '') },
                                                 'attributes': {
-                                                    'geo_lat': { 'values': [ {'double_value': (get_attribute('GEOLAT', sample, 'float', '')) } ] },
-                                                    'geo_long': { 'values': [ {'double_value': (get_attribute('GEOLONG', sample, 'float', '')) } ] },
                                                     'tnm': { 'values': [ { 'string_value': get_attribute('TNM', sample) } ] },
-                                                    # 'age':  { 'values': [ { 'double_value': (get_attribute('AGE', sample, 'float', '')) } ] },
-                                                    'city': { 'values': [ { 'string_value': get_attribute('CITY', sample) } ] },
-                                                    'country': { 'values': [ { 'string_value': country} ] },
                                                     'death': { 'values': [ { 'string_value': get_attribute('DEATH', sample) } ] },
                                                     'followup_months':  { 'values': [ { 'double_value': (get_attribute('FOLLOWUP', sample, 'float', '')) } ] },
                                                     'redirected_to': 'null'