Added documentation and fixed minor bugs and formatting

dbxref/retrieve/eggnog.py

@@ -10,6 +10,7 @@ logger = logging.getLogger(__name__)
 
 
 def main():
+    """main functiion() for script usage"""
     parser = argparse.ArgumentParser(description="Retrieve protein orthology documents from EggNog  and convert them "
                                                  "into json")
     parser.add_argument("--domain", "-d", action="store_true", help="Include a list of PFAM and SMART domains in the "
@@ -33,6 +34,7 @@ def main():
 
 
 def retrieve(dbxrefs, domain, go_terms, tree):
+    """Retrieves data from EggNOG database as json and parses into dbxrefs json format"""
     resolved = dbxref.resolver.resolve(dbxrefs, check_existence=False)
     documents = []
     for entry in resolved:
@@ -52,15 +54,13 @@ def retrieve(dbxrefs, domain, go_terms, tree):
                 try:
                     for pfam_entry in domain_json["domains"]["PFAM"]:
                         pfam_list.append({"protein": pfam_entry[0],
-                                          "1": pfam_entry[1],
-                                          "2": pfam_entry[2],
-                                          "3": pfam_entry[3]
+                                          "sequence count": pfam_entry[1],
+                                          "frequency": pfam_entry[2],
                                           })
                     for smart_entry in domain_json["domains"]["SMART"]:
                         smart_list.append({"protein": smart_entry[0],
-                                           "1": smart_entry[1],
-                                           "2": smart_entry[2],
-                                           "3": smart_entry[3],
+                                           "sequence count": smart_entry[1],
+                                           "frequency": smart_entry[2]
                                            })
                 except KeyError:
                     print(json_url)
@@ -86,25 +86,22 @@ def retrieve(dbxrefs, domain, go_terms, tree):
                     for mol_func_entry in go_term_json["go_terms"]["Molecular Function"]:
                         mol_func.update({mol_func_entry[0]: {"function:": mol_func_entry[1],
                                                              "GO evidence code": mol_func_entry[2],
-                                                             "3": mol_func_entry[3],
-                                                             "4": mol_func_entry[4],
-                                                             "5": mol_func_entry[5]
+                                                             "sequence count": mol_func_entry[3],
+                                                             "frequency": mol_func_entry[4]
                                                              }
                                          })
                     for bio_pro_entry in go_term_json["go_terms"]["Biological Process"]:
                         bio_pro.update({bio_pro_entry[0]: {"process": bio_pro_entry[1],
                                                            "GO evidence code": bio_pro_entry[2],
-                                                           "3": bio_pro_entry[3],
-                                                           "4": bio_pro_entry[4],
-                                                           "5": bio_pro_entry[5]
+                                                           "sequence count": bio_pro_entry[3],
+                                                           "frequency": bio_pro_entry[4]
                                                            }
                                         })
                     for cell_comp_entry in go_term_json["go_terms"]["Cellular Component"]:
                         cell_comp.update({cell_comp_entry[0]: {"component": cell_comp_entry[1],
                                                                "GO evidence code": cell_comp_entry[2],
-                                                               "3": cell_comp_entry[3],
-                                                               "4": cell_comp_entry[4],
-                                                               "5": cell_comp_entry[5]
+                                                               "sequence count": cell_comp_entry[3],
+                                                               "frequency": cell_comp_entry[4]
                                                                }
                                           })
                 except KeyError: