graph-genome#4 Add tests

gfa.py

@@ -3,24 +3,21 @@
 import pickle
 import subprocess
 import io
+import os
 import tempfile
 
 class GFA:
     def __init__(self, gfa: gfapy.Gfa):
         self.gfa = gfa
 
-    @classmethod
-    def load_from_pickle(cls, file: str):
-        #with open(file, 'rb') as pickle_file:
-        gfa = pickle.load(open(file, 'rb'))
-        graph = cls(gfa)
-        return graph
+#    @classmethod
+#    def load_from_pickle(cls, file: str):
+#        graph = pickle.load(open(file, 'rb'))
+#        return graph
 
     @classmethod
     def load_form_xg(cls, file: str, xg_bin: str):
-        #self.gfa = XGWrapper.load(file, xg_bin)
         gfa = gfapy.Gfa()
-        # = subprocess.check_output([xg_bin, "-i", file, "--gfa-out"])
         process = subprocess.Popen([xg_bin, "-i", file, "--gfa-out"], stdout=subprocess.PIPE)
         with io.open(process.stdout.fileno(), closefd=False) as stream:
             [gfa.add_line(line) for line in stream]
@@ -36,18 +33,16 @@ def load_from_gfa(cls, file: str):
         graph = cls(gfa)
         return graph
 
-    def save_as_pickle(self, outfile: str):
-        with open(outfile, 'wb') as pickle_file:
-            pickle.dump(self.gfa, pickle_file)
-#        pickle.dump(self.gfa, file)
+#    def save_as_pickle(self, outfile: str):
+#        with open(outfile, 'wb') as pickle_file:
+#            pickle.dump(self.gfa, pickle_file, protocol=2)
 
     def save_as_xg(self, file: str, xg_bin:str):
-        with tempfile.NamedTemporaryFile(mode="w+") as f:
+        with tempfile.NamedTemporaryFile(mode="w+t", delete=False) as f:
             f.write(self.gfa.to_gfa1_s())
-            process = subprocess.check_output([xg_bin, "-o", file, "-g", f.name])
-        #process = subprocess.Popen([xg_bin, "-o", file, "-g", "-"], stdin=subprocess.PIPE)
-        #output = process.communicate(self.gfa.to_gfa1_s())
-        #return output
+
+        process = subprocess.check_output([xg_bin, "-o", file, "-g", f.name])
+        os.remove(f.name)
 
     def save_as_gfa(self, file:str):
         self.gfa.to_file(file)

test.py

@@ -7,15 +7,13 @@ class GFATest(unittest.TestCase):
 
     def test_gfa(self):
         ### Usage
+        self.maxDiff = None
         location_of_xg = "test/xg"
         graph = GFA.load_from_gfa("test/test.gfa")
         graph.save_as_xg("test/test.xg", location_of_xg)
         graph2 = GFA.load_form_xg("test/test.xg", location_of_xg)
-        graph2.save_as_pickle("test/test.pickle")
-        graph3 = GFA.load_from_pickle("test/test.pickle")
-        self.assertEqual(graph.gfa.to_gfa_1_s, graph3.to_gfa_1_s)
-
-
+        self.assertEqual(len(graph.gfa.to_gfa1_s().split("\n")), len(graph2.gfa.to_gfa1_s().split("\n")))
+
 if __name__ == "__main__":
     unittest.main()        
 

test/test.gfa

@@ -0,0 +1,37 @@
+H	VN:Z:1.0
+P	x	1+,3+,5+,6+,8+,9+,11+,12+,14+,15+	*,*,*,*,*,*,*,*,*
+S	1	CAAATAAG
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+S	2	A
+L	2	+	4	+	0M
+L	2	+	5	+	0M
+S	3	G
+L	3	+	4	+	0M
+L	3	+	5	+	0M
+S	4	T
+L	4	+	6	+	0M
+S	5	C
+L	5	+	6	+	0M
+S	6	TTG
+L	6	+	7	+	0M
+L	6	+	8	+	0M
+S	7	A
+L	7	+	9	+	0M
+S	8	G
+L	8	+	9	+	0M
+S	9	AAATTTTCTGGAGTTCTAT
+L	9	+	10	+	0M
+L	9	+	11	+	0M
+S	10	A
+L	10	+	12	+	0M
+S	11	T
+L	11	+	12	+	0M
+S	12	ATAT
+L	12	+	13	+	0M
+L	12	+	14	+	0M
+S	13	A
+L	13	+	15	+	0M
+S	14	T
+L	14	+	15	+	0M
+S	15	CCAACTCTCTG