parse script for rna localization

issue #58: Table S3 of Atlas of Subcellular RNA Localization Revealed by APEX-Seq

rna_localization/justin_10.1016j.cell.2019.05.027.py

@@ -0,0 +1,56 @@
+import pandas as pd 
+from datanator_query_python.util import mongo_util
+from datanator_query_python.config import config 
+
+
+class RNALocate(mongo_util.MongoUtil):
+    def __init__(self, MongoDB, db, username, password):
+        super().__init__(MongoDB=MongoDB,
+                         db=db,
+                         username=username,
+                         password=password)
+        self.identifier_collection = self.db_obj['identifier']
+        self.observation_collection = self.db_obj['observation']
+
+    def parse_rna_location(self):
+        data = pd.read_excel('mmc3.xlsx', 'Gene lists and orphans')
+        for i in range(len(data)):
+            d = {}
+            d['entity'] = {'type': 'RNA',
+                           'name': data['Common_Gene'][i],
+                           'identifiers': [{'namespace': 'ensembl',
+                                            'value': data['Ensembl_Gene'][i]}]}
+            d['identifier'] = {'namespace': 'ensembl',
+                               'value': data['Ensembl_Gene'][i],
+                               'description': data['Common_Gene'][i]}
+            d['values'] = [{'type': col_name, 'value': data[col_name][i]} for col_name in data.columns[3:11]]
+            d['source'] = [{'namespace': 'doi', 'value': '10.1016/j.cell.2019.05.027'}]
+            d['schema_version'] = '2.0'
+
+            self.observation_collection.update_one({'type': 'RNA',
+                                                   'name': data['Common_Gene'][i],
+                                                   'identifiers': [{'namespace': 'ensembl',
+                                                                     'value': data['Ensembl_Gene'][i]}]},
+                                                    {'$set': d},
+                                                    upsert=True)
+
+            self.identifier_collection.update_one({'namespace': 'ensembl', 'value': data['Ensembl_Gene'][i]},
+                                                  {'$set': {'description': data['Common_Gene'][i]}},
+                                                  upsert=True)
+
+            print("Row {} has been added".format(str(i)))
+
+
+
+def main():
+    conf = config.Justin()
+    username = conf.USERNAME
+    password = conf.PASSWORD
+    MongoDB = conf.SERVER
+    db = 'datanator-demo'
+    #url = 'https://www.cell.com/cms/10.1016/j.cell.2019.05.027/attachment/618723b6-c0fb-4138-846e-fb09eb6b2f2f/mmc3'
+    src = RNALocate(MongoDB, db, username, password)
+    src.parse_rna_location()
+
+if __name__ == "__main__":
+    main()