fixed missing data issue for pantherdb (#155)

src/plugins/pantherdb/parser.py

@@ -1,101 +1,120 @@
-import re
 import os.path
+import re
 
 
 def get_taxid(taxname):
     TAXONOMY = {
-        "ARATH" : 3702,
-        "CAEEL" : 6239,
-        "CHICK" : 9031,
-        "DANRE" : 7955,
-        "DICDI" : 352472,
-        "DROME" : 7227,
-        "ECOLI" : 562,
-        "HUMAN" : 9606,
-        "MOUSE" : 10090,
-        "RAT"   : 10116,
-        "SCHPO" : 4896,
-        "YEAST" : 4932,
+        "ARATH": 3702,
+        "CAEEL": 6239,
+        "CHICK": 9031,
+        "DANRE": 7955,
+        "DICDI": 352472,
+        "DROME": 7227,
+        "ECOLI": 562,
+        "HUMAN": 9606,
+        "MOUSE": 10090,
+        "RAT": 10116,
+        "SCHPO": 4896,
+        "YEAST": 4932,
     }
     return TAXONOMY[taxname]
 
-def load_data (data_folder):
 
+def process_file(data_folder, first):
     data_file = os.path.join(data_folder, "RefGenomeOrthologs")
-
     # this empty dictionary is for storing the final output
     d = {}
     # this empty list is for storing the orthologs of the same reference gene
     o = []
     # this empty list stores the common Uniprot_ID temporarily for comparison
     e = None
 
-    with open(data_file, "r+") as f:# change this to the file name
+    with open(data_file, "r+") as f:  # change this to the file name
         # This function is for splitting the line
         for line in f:
-            y = re.split("[\| \t \n]", line)
-            taxname = y[0]
-            z = re.split("=", y [2])
-            a = re.split("=", y [1])
-            orthtaxname = y[3]
-            b = re.split("=", y [4])
-            c = re.split("=", y [5])
-            ref_gene_uniprot_id = z [1]
-            ref_gene_db_name = a [0]
+
+            y = re.split(r"[\| \t \n]", line)
+
+            if first:
+                taxname = y[0]
+                z = re.split("=", y[2])
+                a = re.split("=", y[1])
+                orthtaxname = y[3]
+                b = re.split("=", y[4])
+                c = re.split("=", y[5])
+            else:
+                orthtaxname = y[0]
+                c = re.split("=", y[2])
+                b = re.split("=", y[1])
+                taxname = y[3]
+                a = re.split("=", y[4])
+                z = re.split("=", y[5])
+
+            ref_gene_uniprot_id = z[1]
+            ref_gene_db_name = a[0]
             ref_gene_db_id = a[-1]
-            ortholog_db_name = b [0]
-            ortholog_db_id = b [-1]
-            ortholog_uniprot_id = c [1]
-            ortholog_type = y [6]
-            ortholog_family = y [8]
+            ortholog_db_name = b[0]
+            ortholog_db_id = b[-1]
+            ortholog_uniprot_id = c[1]
+            ortholog_type = y[6]
+            ortholog_family = y[8]
             _trash = y.pop()
-            assert _trash == ''
+            assert _trash == ""
             ortholog_family = y[-1]
-
             # normalize from ref db so values can be search in other mygene's collections
             if ref_gene_db_name == "MGI":
                 ref_gene_db_id = "MGI:" + ref_gene_db_id
 
-            if e is None: # for the first item
+            if e is None:  # for the first item
                 e = ref_gene_uniprot_id
-                d = { "_id": ref_gene_uniprot_id,
-                       "pantherdb": {
-                       ref_gene_db_name: ref_gene_db_id,
-                       "uniprot_kb": ref_gene_uniprot_id,
-                       }
-                    }
+                d = {
+                    "_id": ref_gene_uniprot_id,
+                    "pantherdb": {
+                        ref_gene_db_name: ref_gene_db_id,
+                        "uniprot_kb": ref_gene_uniprot_id,
+                    },
+                }
 
-            if ref_gene_uniprot_id != e: # if read up to a different ref. gene
-                d ["pantherdb"] ["ortholog"] = o
+            if ref_gene_uniprot_id != e:  # if read up to a different ref. gene
+                d["pantherdb"]["ortholog"] = o
                 yield d
                 e = ref_gene_uniprot_id
-                d = { "_id": ref_gene_uniprot_id,
-                      "pantherdb": {
-                      ref_gene_db_name: ref_gene_db_id,
-                      "uniprot_kb": ref_gene_uniprot_id
-                      }
-                    }
-                new = {ortholog_db_name: ortholog_db_id,
-                       "uniprot_kb": ortholog_uniprot_id,
-                       "ortholog_type": ortholog_type,
-                       "panther_family": ortholog_family,
-                       "taxid": get_taxid(orthtaxname),
-                       }
+                d = {
+                    "_id": ref_gene_uniprot_id,
+                    "pantherdb": {
+                        ref_gene_db_name: ref_gene_db_id,
+                        "uniprot_kb": ref_gene_uniprot_id,
+                    },
+                }
+                new = {
+                    ortholog_db_name: ortholog_db_id,
+                    "uniprot_kb": ortholog_uniprot_id,
+                    "ortholog_type": ortholog_type,
+                    "panther_family": ortholog_family,
+                    "taxid": get_taxid(orthtaxname),
+                }
                 o = [new]
 
-            else: # in this case the ref. gene is the same, just append the ortholog
-                new = {ortholog_db_name: ortholog_db_id,
-                       "uniprot_kb": ortholog_uniprot_id,
-                       "ortholog_type": ortholog_type,
-                       "panther_family": ortholog_family,
-                       "taxid": get_taxid(orthtaxname),
-                       }
+            else:  # in this case the ref. gene is the same, just append the ortholog
+                new = {
+                    ortholog_db_name: ortholog_db_id,
+                    "uniprot_kb": ortholog_uniprot_id,
+                    "ortholog_type": ortholog_type,
+                    "panther_family": ortholog_family,
+                    "taxid": get_taxid(orthtaxname),
+                }
                 o.append(new)
 
-        if o: # for the final item, which does not go to the second "if" route for output
-            d ["pantherdb"] ["ortholog"] = o
-            yield d
+            if (
+                o
+            ):  # for the final item, which does not go to the second "if" route for output
+                d["pantherdb"]["ortholog"] = o
+                yield d
+
 
+def load_data(data_folder):
+    for doc in process_file(data_folder, True):
+        yield doc
 
-if "__name__" == "__main__":
-    g = load_data(data_folder)
+    for doc in process_file(data_folder, False):
+        yield doc