From 0a19fd9638a81b132eb8753bdcf34b92f0f6d079 Mon Sep 17 00:00:00 2001
From: Toshiyuki Yokoyama <yokoyama@no.reply>
Date: Thu, 20 Jun 2019 22:00:36 +0900
Subject: [PATCH] #4 Fix directory

---
 .gitignore           |  4 +++-
 gfa.py => src/gfa.py |  0
 src/graph.py         | 50 ++++++++++++++++++++++++++++++++++++++++++++
 src/test.py          | 20 ++++++++++++++++++
 4 files changed, 73 insertions(+), 1 deletion(-)
 rename gfa.py => src/gfa.py (100%)
 create mode 100644 src/graph.py
 create mode 100644 src/test.py

diff --git a/.gitignore b/.gitignore
index 84a7599..46d43f8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -34,4 +34,6 @@
 # Tests
 test/*.xg
 test/*.pickle
-test/xg
\ No newline at end of file
+test/xg
+
+__pycache__
diff --git a/gfa.py b/src/gfa.py
similarity index 100%
rename from gfa.py
rename to src/gfa.py
diff --git a/src/graph.py b/src/graph.py
new file mode 100644
index 0000000..84bb517
--- /dev/null
+++ b/src/graph.py
@@ -0,0 +1,50 @@
+from typing import List, NamedTuple
+import pickle
+
+class PathIndex(NamedTuple):
+    node: Node
+    index: int
+
+class Graph:
+    version = 1.0
+    def __init__(self, nodes: list(Nodes), paths: list(Paths)):
+        self.nodes = nodes
+        self.paths = paths
+
+    def load_from_pickle(self, file: str):
+        self = pickle.load(file)
+
+    def load_form_xg(self, file: str, xg_bin: str):
+        raise NotImplementedError()
+
+    def dump():
+        raise NotImplementedError()
+
+    def save_as_pickle():
+        pickle.dump(self, file)
+
+    def save_as_xg():
+        raise NotImplementedError()
+
+class Node:
+    def __init__(self, id: int, sequence: str, paths: list(PathIndex)):
+        self.id = id
+        self.sequence = sequence
+        self.paths = paths
+        #self.strand = strand
+    
+    def alternative_nodes(self):
+        #WIP
+
+class Path:
+    def __init__(self, name: str, nodes: list(Node)):
+        self.name = name
+        self.nodes = paths
+
+if __name__ == "__main__":
+    location_of_xg = sys.argv[0]
+
+    ### Usage
+    graph = Graph.load_form_xg
+    graph.save_as_pickle()
+
diff --git a/src/test.py b/src/test.py
new file mode 100644
index 0000000..0386258
--- /dev/null
+++ b/src/test.py
@@ -0,0 +1,20 @@
+import unittest
+from gfa import GFA
+
+class GFATest(unittest.TestCase):
+    """ test class of gfa.py
+    """
+
+    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)
+        self.assertEqual(len(graph.gfa.to_gfa1_s().split("\n")), len(graph2.gfa.to_gfa1_s().split("\n")))
+ 
+if __name__ == "__main__":
+    unittest.main()        
+
+