#!/usr/bin/env python
# coding: utf-8

# In[1]:


def de_bruijn_ize(st, k):
    """ Return a list holding, for each k-mer, its left
        k-1-mer and its right k-1-mer in a pair """
    edges = []
    nodes = set()
    for i in range(len(st) - k + 1):
        edges.append((st[i:i+k-1], st[i+1:i+k]))
        nodes.add(st[i:i+k-1])
        nodes.add(st[i+1:i+k])
    return nodes, edges


# In[2]:


nodes, edges = de_bruijn_ize("ACGCGTCG", 3)


# In[3]:


nodes 


# In[4]:


edges 


# In[5]:


def visualize_de_bruijn(st, k):
    """ Visualize a directed multigraph using graphviz """
    nodes, edges = de_bruijn_ize(st, k)
    dot_str = 'digraph "DeBruijn graph" {\n'
    for node in nodes:
        dot_str += '  %s [label="%s"] ;\n' % (node, node)
    for src, dst in edges:
        dot_str += '  %s -> %s ;\n' % (src, dst)
    return dot_str + '}\n'


# In[6]:


# might have to do this first:
# %install_ext https://raw.github.com/cjdrake/ipython-magic/master/gvmagic.py
get_ipython().run_line_magic('load_ext', 'gvmagic')


# In[7]:


get_ipython().run_line_magic('dotstr', 'visualize_de_bruijn("ACGCGTCG", 3)')