https://github.com/fenderglass/Ragout
Revision 93ad1789e197c609135838d3bbb380714aeb3bd1 authored by fenderglass on 03 August 2013, 10:52:27 UTC, committed by fenderglass on 03 August 2013, 10:52:27 UTC
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Tip revision: 93ad1789e197c609135838d3bbb380714aeb3bd1 authored by fenderglass on 03 August 2013, 10:52:27 UTC
initial commit
initial commit
Tip revision: 93ad178
bg.py
#!/usr/bin/env python
import sys
import math
from collections import namedtuple, defaultdict
Edge = namedtuple("Edge", ["vertex", "color"])
Colors = ["red", "green", "blue", "yellow", "black"]
Link = namedtuple("Link", ["vertex", "sign"])
#Scaffold = namedtuple("Scaffold", ["left", "right", "contigs"])
class Node:
def __init__(self):
self.edges = []
class Contig:
def __init__(self, name):
self.name = name
self.sign = 1
self.inverse = False
self.blocks = []
class Scaffold:
def __init__(self, left, right, contigs):
self.left = left
self.right = right
self.contigs = contigs
def parse_permutations_file(filename):
graph = defaultdict(Node)
contigs = []
fin = open(filename, "r")
color = 0
contig_name = None
for line in fin:
if line.startswith(">"):
contig_name = line.strip()[1:] if line.startswith(">contig") else None
continue
blocks = line.strip().split(" ")[0:-1]
if contig_name:
contig = Contig(contig_name)
contig.blocks = map(int, blocks)
contigs.append(contig)
continue
#not a contig
for i in xrange(len(blocks) - 1):
l = int(blocks[i])
r = int(blocks[i + 1])
graph[-l].edges.append(Edge(r, color))
graph[r].edges.append(Edge(-l, color))
color += 1
return graph, contigs
def build_contig_index(contigs):
index = defaultdict(list)
for i, c in enumerate(contigs):
for block in c.blocks:
index[abs(block)].append(i)
return index
def sign(val):
return math.copysign(1, val)
def get_scaffolds(contigs, connections):
contig_index = build_contig_index(contigs)
scaffolds = []
visited = set()
def extend_scaffold(contig):
visited.add(contig)
scf = Scaffold(contig.blocks[0], contig.blocks[-1], [contig])
scaffolds.append(scf)
#go right
while abs(scf.right) in connections:
adjacent = connections[abs(scf.right)]
assert len(contig_index[adjacent.vertex]) == 1
contig = contigs[contig_index[adjacent.vertex][0]]
if contig in visited:
break
if abs(contig.blocks[0]) == adjacent.vertex:
scf.contigs.append(contig)
scf.contigs[-1].sign = sign(scf.right * contig.blocks[0] * adjacent.sign)
scf.right = contig.blocks[-1] * scf.contigs[-1].sign
visited.add(contig)
elif abs(contig.blocks[-1]) == adjacent.vertex:
scf.contigs.append(contig)
scf.contigs[-1].sign = sign(scf.right * contig.blocks[-1] * adjacent.sign)
scf.contigs[-1].inverse = True
scf.right = contig.blocks[0] * scf.contigs[-1].sign
visited.add(contig)
#go left
while abs(scf.left) in connections:
adjacent = connections[abs(scf.left)]
assert len(contig_index[adjacent.vertex]) == 1
contig = contigs[contig_index[adjacent.vertex][0]]
if contig in visited:
break
if abs(contig.blocks[-1]) == adjacent.vertex:
scf.contigs.insert(0, contig)
scf.contigs[0].sign = sign(scf.left * contig.blocks[-1] * adjacent.sign)
scf.left = contig.blocks[0] * scf.contigs[0].sign
visited.add(contig)
elif abs(contig.blocks[0]) == adjacent.vertex:
scf.contigs.insert(0, contig)
scf.contigs[0].sign = sign(scf.left * contig.blocks[0] * adjacent.sign)
scf.contigs[0].inverse = True
scf.left = contig.blocks[-1] * scf.contigs[0].sign
visited.add(contig)
for contig in contigs:
if contig not in visited:
extend_scaffold(contig)
return scaffolds
def simple_connections(graph, contigs):
NUM_REF = 4 #hardcode!
connections = {}
for block in graph:
#look into breakpoint graph
edges = map(lambda e: e.vertex, graph[block].edges)
#only cases with connected component of 2 nodes
if edges.count(edges[0]) == NUM_REF == len(edges):
back_edges = map(lambda e: e.vertex, graph[edges[0]].edges)
if back_edges.count(block) == NUM_REF == len(back_edges):
s = sign(-block * edges[0])
connections[abs(block)] = Link(vertex=abs(edges[0]), sign=s)
connections[abs(edges[0])] = Link(vertex=abs(block), sign=s)
for scf in get_scaffolds(contigs, connections):
for contig in scf.contigs:
if not contig.inverse:
print map(lambda b: int(b * contig.sign), contig.blocks),
else:
print map(lambda b: int(b * contig.sign), contig.blocks)[::-1],
print ""
def output_graph(graph, dot_file):
dot_file.write("graph {\n")
used_vertexes = set()
for node_id, node in graph.iteritems():
for edge in node.edges:
if edge.vertex not in used_vertexes:
dot_file.write("""{0} -- {1} [color = "{2}"];\n"""
.format(node_id, edge.vertex, Colors[edge.color]))
used_vertexes.add(node_id)
#for i in xrange(max(graph.keys()) + 1):
# dot_file.write("""{0} -- {1} [color = "black"];\n""".format(i, -i))
dot_file.write("}")
if __name__ == "__main__":
graph, contigs = parse_permutations_file(sys.argv[1])
simple_connections(graph, contigs)
#output_graph(graph, open("bg.dot", "w"))
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