add some examples of how to use the python library

examples/explore.py

@@ -0,0 +1,86 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+# this shows some examples of how to use the python bindings to odgi
+
+import sys
+if len(sys.argv) is 1:
+    print("usage: PYTHONPATH=../lib", sys.argv[0], "graph.og")
+    print("displays information about the graph, and iterates over it")
+    print("to build the input graph, use `odgi build -g graph.gfa -o graph.og`")
+    exit(1)
+
+import odgi
+
+g = odgi.graph()
+g.load(sys.argv[1])
+
+# the number of nodes and edges is given
+print("node count:", g.get_node_count())
+print("path count:", g.get_path_count())
+
+# iterate over the nodes and sum the sequence length
+# we have to use a counter object to count
+# because in python you can't assign inside lambdas 🤦
+# and there are no true closures over local variables 😭
+class counter:
+    total = 0
+    def add(self, l):
+        self.total += l
+s = counter()
+g.for_each_handle(lambda h: s.add(g.get_length(h)))
+print("graph length:", s.total)
+
+# iterate over the handles and use follow_edges to list the edges
+def show_edge(a, b):
+    print(g.get_id(a), "-->", g.get_id(b))
+
+def display_node_edges(h):
+    print("node", g.get_id(h))
+    g.follow_edges(
+        h, False,
+        lambda n:
+        show_edge(h, n))
+    g.follow_edges(
+        h, True,
+        lambda n:
+        show_edge(n, h))
+
+# displays all the edges twice, once for each of their ends
+g.for_each_handle(display_node_edges)
+
+# count all the edges
+e = counter()
+def handle_edges(h):
+    g.follow_edges(h, True, lambda x: e.add(1))
+
+g.for_each_handle(handle_edges)
+print("edge count", e.total)
+print("edges/node", float(e.total) / float(g.get_node_count()))
+print("bp/edge", float(s.total) / float(e.total))
+
+# getting path names from path handles
+path_names = []
+g.for_each_path_handle(lambda p: path_names.append(g.get_path_name(p)))
+print(path_names)
+
+
+# getting the path handle from a path name
+print([g.get_path_handle(name) for name in path_names])
+
+# print a string representing each step
+# this shows the path and orientation relative to the handle
+def step_str(step):
+    #id_str = str(g.get_id(g.get_handle_of_step(step)))
+    path_str = g.get_path_name(g.get_path_handle_of_step(step))
+    dir_str = "+" if not g.get_is_reverse(g.get_handle_of_step(step)) else "-"
+    return path_str + dir_str
+
+# getting the steps on each handle
+def show_steps(handle):
+    steps = []
+    g.for_each_step_on_handle(handle, lambda step: steps.append(step))
+    print("node:", g.get_id(handle), "steps:", " ".join([step_str(s) for s in steps]))
+
+g.for_each_handle(show_steps)
+