fixing line count to reflect gaf or gpad as appropriate

bin/README.md

@@ -3,6 +3,6 @@ See [command line docs](http://ontobio.readthedocs.io/en/latest/commandline.html
 To test validate.py on a particular source:
 ```bash
 poetry install
-poetry run validate produce -m ../go-site/metadata --gpad -t [path/to/local/ontobio/checkout] -o go-basic.json --only-dataset mgi MGI
-poetry run validate produce -m ../go-site/metadata --gpad -t [path/to/local/ontobio/checkout] -o go-basic.json --only-dataset goa_chicken goa
+poetry run validate produce -m ../go-site/metadata --gpad -t [path/to/local/ontobio/clone] -o go-basic.json --only-dataset mgi MGI
+poetry run validate produce -m ../go-site/metadata --gpad -t [path/to/local/ontobio/clone] -o go-basic.json --only-dataset goa_chicken goa
 ```

bin/validate.py

@@ -343,8 +343,6 @@ def make_gpads(dataset, gaf_path, products, ontology_graph, noctua_gpad_file):
         # Bail if we have no products
         return []
 
-    with open(gaf_path) as sg:
-        lines = sum(1 for line in sg)
 
     # logger.info("AssocParserConfig used: {}".format(config))
     split_source = os.path.split(gaf_path)[0]
@@ -354,6 +352,10 @@ def make_gpads(dataset, gaf_path, products, ontology_graph, noctua_gpad_file):
 
     print("noctua-gpad-file: {}".format(noctua_gpad_file))
     if noctua_gpad_file is not None:
+
+        with open(noctua_gpad_file) as sg:
+            lines = sum(1 for line in sg)
+
         with open(noctua_gpad_file) as nf:
             gpadparser = GpadParser(config=assocparser.AssocParserConfig(
                 ontology=ontology_graph,
@@ -365,6 +367,9 @@ def make_gpads(dataset, gaf_path, products, ontology_graph, noctua_gpad_file):
                 for association in associations:
                     gpadwriter.write_assoc(association)
 
+    with open(gaf_path) as sg:
+        lines = sum(1 for line in sg)
+
     with open(gaf_path) as gf:
         gafparser = GafParser(config=assocparser.AssocParserConfig(
             ontology=ontology_graph,