Added test to demonstrate the use of the new args in the write_hier f…

…unction in the GODag class.

tests/test_write_hier.py

@@ -0,0 +1,62 @@
+
+
+import sys
+
+# Test local version of goatools
+sys.path.insert(0, '..')
+
+from goatools.obo_parser import GODag
+
+
+def test_write_hier_all(dag, out):
+  """Prints the entire mini GO hierarchy, with counts of children."""
+  out.write('\nTEST ALL: Print all hierarchies:\n')
+  dag.write_hier( "GO:0000001", out, num_child=True)
+
+
+def test_write_hier_norep(dag, out):
+  """Shortens hierarchy report by only printing branches once.
+
+       Prints the 'entire hierarchy' of GO:0000005 the 1st time seen:
+
+         ---     1 GO:0000005    L-02    D-02
+         ----     0 GO:0000010   L-03    D-04
+
+       Prints just GO:0000005 (ommit child GO:10) the 2nd time seen:
+
+         ===     1 GO:0000005    L-02    D-02
+  
+       '=' is used in hierarchy mark to indicate that the pathes
+           below the marked term have already been printed.
+  """
+  out.write('\nTEST ALL: Print branches just once:\n')
+  dag.write_hier( "GO:0000001", out, num_child=True, short_prt=True)
+
+
+def test_write_hier_lim(dag, out):
+  """Limits hierarchy list to GO Terms specified by user.
+  """
+  go_omit = ['GO:0000005', 'GO:0000010']
+  go_ids = [go_id for go_id in dag if go_id not in go_omit]
+  out.write('\nTEST OMIT: 05->10:\n')
+  dag.write_hier( "GO:0000001", out, include_only=go_ids)
+    #go_marks=[oGO.id for oGO in oGOs_in_cluster])
+
+
+def test_write_hier_mrk(dag, out):
+  """Print all paths, but mark GO Terms of interest. """
+  mark_lst = ['GO:0000001', 'GO:0000003', 'GO:0000006', 'GO:0000008', 'GO:0000009']
+  out.write('\nTEST MARK: 01->03->06->08->09:\n')
+  dag.write_hier( "GO:0000001", out, go_marks=mark_lst)
+    #go_marks=[oGO.id for oGO in oGOs_in_cluster])
+
+def test_all():
+  dag = GODag("./data/mini_obo.obo")  
+  out = sys.stdout
+  test_write_hier_all(dag, out)
+  test_write_hier_norep(dag, out)
+  test_write_hier_lim(dag, out)
+  test_write_hier_mrk(dag, out)
+
+if __name__ == '__main__':
+  test_all()