Adds taxonomyID of non-human organisms

DaddyWesker · Apr 22, 2020 · 7127df9 · 7127df9
1 parent 8243075
commit 7127df9
Showing 1 changed file with 18 additions and 16 deletions.
diff --git a/coronavirus_biogrid.py b/coronavirus_biogrid.py
@@ -33,16 +33,16 @@ def evaLink(node1, node1_type, node2, node2_type, predicate, prefix1="", prefix2
         return ("(EvaluationLink {}\n".format(stv) +
             "\t (PredicateNode \""+ predicate + "\")\n" +
             "\t ({} \n".format(list_type) +
-            "\t\t ({}".format(node1_type) + " \"" + prefix1 + node1 + "\")\n" +
-            "\t\t ({}".format(node2_type) + " \"" + prefix2 + node2 + "\")))\n" )
+            "\t\t ({}".format(node1_type) + " \"" + prefix1 + str(node1) + "\")\n" +
+            "\t\t ({}".format(node2_type) + " \"" + prefix2 + str(node2) + "\")))\n" )
     else:
         return ""
 
 def member(node1, node1_type, node2, node2_type, prefix1="", prefix2=""):
     if not (str(node1) in ["-", "nan"] or str(node2) in ["-", "nan"]):
         return ('(MemberLink\n' + 
-                '\t({} "'.format(node1_type) + prefix1 + node1 + '")\n'+
-                '\t({} "'.format(node2_type) + prefix2 + node2 + '"))\n')
+                '\t({} "'.format(node1_type) + prefix1 + str(node1) + '")\n'+
+                '\t({} "'.format(node2_type) + prefix2 + str(node2) + '"))\n')
     else:
         return ""
 
@@ -96,7 +96,8 @@ def import_data(data, source, version, gene_level=False, form='tab2'):
                 entrez1 = str(data.iloc[i]['Entrez Gene Interactor A']).strip()
                 entrez2 = str(data.iloc[i]['Entrez Gene Interactor B']).strip()
                 stv = '(stv 1.0 {})'.format(score)
-
+                taxonomy_id_1 = int(data.iloc[i]['Organism Interactor A'])
+                taxonomy_id_2 = int(data.iloc[i]['Organism Interactor B'])
 
                 if (gene1, gene2) not in pairs or (gene2, gene1) not in genes:
                     if not gene1 in entrez:
@@ -123,25 +124,26 @@ def import_data(data, source, version, gene_level=False, form='tab2'):
                         f.write(evaLink(gene2, "GeneNode", bio,"ConceptNode", "has_biogridID", prefix2="Bio:"))
                         f.write(evaLink(prot2, "MoleculeNode", bio,"ConceptNode", "has_biogridID", prefix1="Uniprot:",prefix2="Bio:"))
 
-                    if gene1 not in genes and int(data.iloc[i]['Organism Interactor A']) == 2697049: 
-                        f.write(evaLink(gene1, "GeneNode", "SARS-CoV-2" , "ConceptNode","has_organism"))
-                        f.write(evaLink(prot1, "MoleculeNode", "SARS-CoV-2", "ConceptNode","has_organism", prefix1="Uniprot:"))
+                    if gene1 not in genes and taxonomy_id_1 == 2697049: 
+                        f.write(evaLink(gene1, "GeneNode", taxonomy_id_1 , "ConceptNode","from_organism", prefix2="TaxonomyID:"))
+                        f.write(evaLink(prot1, "MoleculeNode", taxonomy_id_1, "ConceptNode","from_organism", prefix1="Uniprot:",prefix2="TaxonomyID:"))
                         if gene_level:
-                            g.write(evaLink(gene1, "GeneNode", "SARS-CoV-2" , "ConceptNode","has_organism"))
-                            g.write(evaLink(prot1, "MoleculeNode", "SARS-CoV-2", "ConceptNode","has_organism", prefix1="Uniprot:"))
-                    if gene2 not in genes and int(data.iloc[i]['Organism Interactor B']) != 9606:
-                        f.write(evaLink(gene2, "GeneNode", "SARS-CoV-2" , "ConceptNode","has_organism"))
-                        f.write(evaLink(prot2, "MoleculeNode", "SARS-CoV-2", "ConceptNode","has_organism", prefix1="Uniprot:"))
+                            g.write(evaLink(gene1, "GeneNode", taxonomy_id_1 , "ConceptNode","from_organism",prefix2="TaxonomyID:"))
+                            g.write(evaLink(prot1, "MoleculeNode", taxonomy_id_1, "ConceptNode","from_organism", prefix1="Uniprot:", prefix2="TaxonomyID:"))
+                    if gene2 not in genes and taxonomy_id_2 == 2697049:
+                        f.write(evaLink(gene2, "GeneNode", taxonomy_id_2 , "ConceptNode","from_organism",prefix2="TaxonomyID:"))
+                        f.write(evaLink(prot2, "MoleculeNode", taxonomy_id_2, "ConceptNode","from_organism", prefix1="Uniprot:",prefix2="TaxonomyID:"))
                         if gene_level:
-                            g.write(evaLink(gene2, "GeneNode", "SARS-CoV-2" , "ConceptNode", "has_organism"))
-                            g.write(evaLink(prot2, "MoleculeNode", "SARS-CoV-2", "ConceptNode", "has_organism", prefix1="Uniprot:"))                            
+                            g.write(evaLink(gene2, "GeneNode", taxonomy_id_2 , "ConceptNode", "from_organism", prefix2="TaxonomyID:"))
+                            g.write(evaLink(prot2, "MoleculeNode", taxonomy_id_2, "ConceptNode", "from_organism", prefix1="Uniprot:", prefix2="TaxonomyID:"))                            
 
                     genes.append(gene1)
                     genes.append(gene2)
                     proteins.append(prot1)
                     proteins.append(prot2)
                     pairs.append((gene1,gene2))
-
+        f.write(evaLink("2697049", "ConceptNode", "SARS-CoV-2", "ConceptNode","has_name",prefix1="TaxonomyID:"))
+        g.write(evaLink("2697049", "ConceptNode", "SARS-CoV-2", "ConceptNode","has_name",prefix1="TaxonomyID:"))
     pairs = set((a,b) if a<=b else (b,a) for a,b in pairs)
     number_of_interactions = len(pairs)
     script = "https://github.com/MOZI-AI/knowledge-import/coronavirus_biogrid.py"