#4: Debug of dp conditions

graph-genome · Jul 9, 2019 · 1321465 · 1321465
1 parent 205e2bc
commit 1321465
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Showing 4 changed files with 60 additions and 9 deletions.
diff --git a/src/sort.py b/src/sort.py
@@ -46,28 +46,28 @@ def lcs(self, s1: List[Profile], s2: Path) -> List[Profile]:
         index = []
         prev = set()
 
-        while i > 0 or j > 0:
+        while i > 0 and j > 0:
             if s1[i-1].node == s2.nodes[j-1]:
                 prev_paths = s1[i-1].paths
                 prev_paths.append(s2)
-                index.append(Profile(s1[i-1].node, prev_paths, s1[i-1].node in prev))
-                prev.add(s1[i-1].node)
+                index.append(Profile(s1[i-1].node, prev_paths, s1[i-1].node.node.index in prev))
+                prev.add(s1[i-1].node.node.index)
                 i -= 1
                 j -= 1
             elif dp[i-1][j] > dp[i][j-1]:
                 prev_paths = s1[i-1].paths
-                index.append(Profile(s1[i-1].node, prev_paths, s1[i-1].node in prev))
-                prev.add(s1[i-1].node)
+                index.append(Profile(s1[i-1].node, prev_paths, s1[i-1].node.node.index in prev))
+                prev.add(s1[i-1].node.node.index)
                 i -= 1
             else:
                 index.append(Profile(s2.nodes[j-1], [s2], False))
-                prev.add(s2.nodes[j-1])
+                prev.add(s2.nodes[j-1].node.index)
                 j -= 1
 
         while i > 0:
             prev_paths = s1[i - 1].paths
-            index.append(Profile(s1[i - 1].node, prev_paths, s1[i - 1].node in prev))
-            prev.add(s1[i - 1].node)
+            index.append(Profile(s1[i - 1].node, prev_paths, s1[i - 1].node.node.index in prev))
+            prev.add(s1[i - 1].node.node.index)
             i -= 1
 
         while j > 0:
@@ -83,6 +83,7 @@ def lcs(self, s1: List[Profile], s2: Path) -> List[Profile]:
     def to_graph(self):
         factory_input = []
         current_slice = Slice([])
+        print(self.profile)
         for prof in self.profile:
             paths = [x.name for x in prof.paths]
             if len(prof.paths) == len(self.paths):

diff --git a/src/test.py b/src/test.py
@@ -69,6 +69,18 @@ def test_dagify(self):
         z = 'z'
         self.assertEqual(graph, graph_by_toplogical_sort)
 
+    def test_dagify2(self):
+        gfa = GFA.load_from_gfa("../test/test2.gfa")
+        paths = gfa.to_paths
+        dagify = DAGify(paths)
+        dagify.recursive_merge(0)
+        graph = dagify.to_graph()
+
+        graph_by_toplogical_sort = gfa.to_graph
+        x = 'x'
+        y = 'y'
+        z = 'z'
+        self.assertEqual(graph, graph_by_toplogical_sort)
 
 class GFATest(unittest.TestCase):
     """ test class of gfa.py

diff --git a/test/test2.gfa b/test/test2.gfa
@@ -2,7 +2,7 @@ H	VN:Z:1.0
 P	x	1+,3+,5+,6+,8+,9+,11+,12+,14+,15+	*,*,*,*,*,*,*,*,*
 P	y	1+,2+,5+,6+,8+,9+,11+,12+,14+,15+	*,*,*,*,*,*,*,*,*
 P	z	1+,2+,4+,6+,7+,9+,10+,12+,14+,15+	*,*,*,*,*,*,*,*,*
-P	a	12+,13+,15+	*,*
+P	a	7+,9+,10+	*,*
 S	1	CAAATAAG
 L	1	+	2	+	0M
 L	1	+	3	+	0M

diff --git a/test/test3.gfa b/test/test3.gfa
@@ -0,0 +1,38 @@
+H	VN:Z:1.0
+P	x	1+,3+,5+,6+,8+,9+,11+,12+,14+,15+	*,*,*,*,*,*,*,*,*
+P	y	1+,15+,5+,6+,8+,9+,11+,12+,14+,15+	*,*,*,*,*,*,*,*,*
+S	1	CAAATAAG
+L	1	+	15	+	0M
+L	1	+	3	+	0M
+S	2	A
+L	2	+	4	+	0M
+L	15	+	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