Merge 01109d9 into 1a0a7ba

Knowledge-Graph-Hub · Jun 27, 2020 · 05742d3 · 05742d3
2 parents 1a0a7ba + 01109d9
commit 05742d3
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Showing 2 changed files with 27 additions and 2 deletions.
diff --git a/download.yaml b/download.yaml
@@ -114,7 +114,7 @@
 -
   # Gene Product information for SARS-CoV-2 genes in GPI format
   # http://geneontology.org/docs/gene-product-information-gpi-format/
-  url: ftp://ftp.ebi.ac.uk/pub/contrib/goa/uniprot_sars-cov-2.gpi
+  url: https://raw.githubusercontent.com/Knowledge-Graph-Hub/kg-covid-19/master/curated/ORFs/uniprot_sars-cov-2.gpi
   local_name: uniprot_sars-cov-2.gpi
 
 #

diff --git a/kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.py b/kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.py
@@ -54,17 +54,42 @@ def run(self, data_file: str = None):
             # write headers
             node.write("\t".join(self.node_header) + "\n")
             edge.write("\t".join(self.edge_header) + "\n")
-
+            seen = set()
             with open(gpi_file, 'r') as gpi_fh:
                 for rec in _gpi12iterator(gpi_fh):
                     node_data = self.gpi_to_gene_node_data(rec)
+                    seen.add(node_data[0])
                     write_node_edge_item(node, self.node_header, node_data)
 
             with open(gpa_file, 'r') as gpa_fh:
                 for rec in _gpa11iterator(gpa_fh):
                     edge_data = self.gpa_to_edge_data(rec)
+                    subject_node = edge_data[0]
+                    if subject_node not in seen:
+                        subject_node_data = [subject_node, self.guess_category(subject_node)] + [""] * 4 + [self.source_name]
+                        write_node_edge_item(node, self.node_header, subject_node_data)
+                        seen.add(subject_node)
+                    object_node = edge_data[2]
+                    if object_node not in seen:
+                        object_node_data = [object_node, self.guess_category(object_node)] + [""] * 4 + [self.source_name]
+                        write_node_edge_item(node, self.node_header, object_node_data)
+                        seen.add(object_node)
+
                     write_node_edge_item(edge, self.edge_header, edge_data)
 
+    def guess_category(self, identifier):
+        """Guess category for a given identifier.
+
+        """
+        prefix = identifier.split(':')[0]
+        if prefix in {'UniProtKB', 'ComplexPortal'}:
+            category = 'biolink:Protein'
+        elif prefix in {'GO'}:
+            category = 'biolink:OntologyClass'
+        else:
+            category = 'biolink:NamedThing'
+        return category
+
     def gpa_to_edge_data(self, rec: dict) -> list:
         """given a parsed gpa entry, return an edge with the annotations