From e5c617260e480d180bfa93bd3b2a2bdbe7319cca Mon Sep 17 00:00:00 2001
From: Toshiyuki Yokoyama <yokoyama@no.reply>
Date: Tue, 2 Jul 2019 23:07:05 +0900
Subject: [PATCH] #4: Add paths to graph class
---
src/gfa.py | 3 +--
src/graph.py | 45 ++++++++++++++++++++++++---------------------
src/test.py | 2 +-
test/test2.gfa | 2 +-
4 files changed, 27 insertions(+), 25 deletions(-)
diff --git a/src/gfa.py b/src/gfa.py
index e54d9c1..f4e64ba 100644
--- a/src/gfa.py
+++ b/src/gfa.py
@@ -117,7 +117,7 @@ def from_graph(cls, graph: Graph):
path_list[path].append(segment_id)
for path_key in path_list:
path_values = [str(x) for x in path_list[path_key]]
- gfa.add_line('\t'.join(['P', path_key, "+,".join(path_values)+"+", ",".join(['*' for x in path_values])]))
+ gfa.add_line('\t'.join(['P', path_key, "+,".join(path_values)+"+", ",".join(['*' for _ in path_values])]))
return cls(gfa)
@property
@@ -128,7 +128,6 @@ def to_graph(self):
# Extract all paths into graph
for path in self.gfa.paths:
- ### TODO: Replace it as a path class object.
for node in path.segment_names:
path_dict[node.name + node.orient].append(path.name)
for node_pair in pairwise(path.segment_names):
diff --git a/src/graph.py b/src/graph.py
index f406623..68d5001 100644
--- a/src/graph.py
+++ b/src/graph.py
@@ -107,10 +107,33 @@ def smallest(self):
version = 1.0
+class NodeIndex(NamedTuple):
+ node: Node
+ strand: str
+
+class Path:
+ """TODO: Paths have not been implemented yet."""
+ def __init__(self, name: str, nodes: List[NodeIndex]):
+ self.name = name
+ self.nodes = nodes
+ self.position_checkpoints = {}
+
+ def __getitem__(self, i):
+ return self.nodes[i]
+
+ def __repr__(self):
+ """Warning: the representation strings are very sensitive to whitespace"""
+ return self.nodes.__repr__()
+
+ def to_gfa(self):
+ return '\t'.join(['P', self.name, "+,".join([x.node.name + x.strand for x in self.nodes])+"+", ",".join(['*' for x in self.nodes])])
+
+
class Graph:
- def __init__(self, cmd: List):
+ def __init__(self, cmd: List, paths: List[Path] = []):
"""Factory for generating graphs from a representation"""
self.slices = []
+ self.paths = paths
if isinstance(cmd, str):
cmd = eval(cmd)
for sl in cmd:
@@ -159,26 +182,6 @@ def save_as_pickle(self, file):
def save_as_xg(self):
raise NotImplementedError()
-class NodeIndex(NamedTuple):
- node: Node
- strand: str
-
-class Path:
- """TODO: Paths have not been implemented yet."""
- def __init__(self, name: str, nodes: List[NodeIndex]):
- self.name = name
- self.nodes = nodes
- self.position_checkpoints = {}
-
- def __getitem__(self, i):
- return self.nodes[i]
-
- def __repr__(self):
- """Warning: the representation strings are very sensitive to whitespace"""
- return self.nodes.__repr__()
-
- def to_gfa(self):
- return '\t'.join(['P', self.name, "+,".join([x.node.name + x.strand for x in self.nodes])+"+", ",".join(['*' for x in self.nodes])])
if __name__ == "__main__":
location_of_xg = sys.argv[0]
diff --git a/src/test.py b/src/test.py
index cf2e819..e740131 100644
--- a/src/test.py
+++ b/src/test.py
@@ -121,7 +121,7 @@ def is_different(gfa1, gfa2):
if l.line.from_segment.name != l2.line.from_segment.name:
print(l, l2)
different = True
- if l.line.to_segment.name != l.line.to_segment.name:
+ if l.line.to_segment.name != l2.line.to_segment.name:
print(l, l2)
different = True
for s in gfa1.edges:
diff --git a/test/test2.gfa b/test/test2.gfa
index 5a01b3e..52164c1 100644
--- a/test/test2.gfa
+++ b/test/test2.gfa
@@ -1,7 +1,7 @@
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+,5+,6+,7+,9+,11+,12+,14+,15+ *,*,*,*,*,*,*,*,*
+P z 1+,2+,4+,6+,7+,9+,10+,12+,14+,15+ *,*,*,*,*,*,*,*,*
P a 12+,13+,15+ *,*
S 1 CAAATAAG
L 1 + 2 + 0M