Merge pull request #684 from biolink/pipeline-issue-383

fixes pipeline issue 383 - gpad 1.2 should have `!gpa-version` in the header, not `!gpad-version` in the header

ontobio/io/assocwriter.py

@@ -119,11 +119,14 @@ def __init__(self, file=None, version=None):
         click.echo("Writing GPAD version: {}".format(version))
         if version in [GPAD_1_2, GPAD_2_0]:
             self.version = version
+            if version == GPAD_1_2:
+                self._write("!gpa-version: {}\n".format(self.version))
+            else:
+                self._write("!gpad-version: {}\n".format(self.version))
         else:
             self.version = GPAD_1_2
+            self._write("!gpa-version: {}\n".format(self.version))
 
-        self._write("!gpad-version: {}\n".format(self.version))
-        click.echo("Writing GPAD version: {}".format(self.version))
         self._write("!generated-by: {}\n".format("GO Central"))
         self._write("!date-generated: {}\n".format(str(datetime.datetime.now().strftime("%Y-%m-%dT%H:%M"))))
         self.ecomap = ecomap.EcoMap()
@@ -149,10 +152,10 @@ class GafWriter(AssocWriter):
     This converts an association dictionary object as produced in GafParser or
     GpadParser into a GAF line.
 
-    The GAF Writer now assumes that it is writing out GAF version 2.1 style
+    The GAF Writer now assumes that it is writing out GAF version 2.2 style
     annotations. The version can be set when creating a new GafWriter to 2.2
     with `version=2.2`. If any version other than 2.1 or 2.2, GafWriter will
-    default to 2.1.
+    default to 2.2.
 
     The only difference in 2.1 and 2.2 are how qualifiers (column 4) are handled.
     GAF 2.1 allows empty or only `NOT` qualifier values, and only allows
@@ -167,7 +170,7 @@ class GafWriter(AssocWriter):
     written out, or if the qualifier is empty and 2.2 is being written.
     """
 
-    def __init__(self, file=None, source=None, version="2.1"):
+    def __init__(self, file=None, source=None, version="2.2"):
         self.file = file
         if version in ["2.1", "2.2"]:
             self.version = version

tests/test_gpad_writer.py

@@ -18,7 +18,7 @@ def test_gpad_iba_writing():
     outlines = out.getvalue().split("\n")
 
     print(outlines)
-    assert outlines[0] == "!gpad-version: 1.2"
+    assert outlines[0] == "!gpa-version: 1.2"
     assert outlines[1] == "!generated-by: GO Central"
     assert outlines[2].startswith("!date-generated:")
     assert outlines[3] == "WB\tWBGene00022144\tpart_of\tGO:0005886\tPMID:21873635\tECO:0000318\tPANTHER:PTN000073732|RGD:3252\t\t20180308\tGO_Central\t\t"