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filter_cluster.py
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filter_cluster.py
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#!/usr/bin/env python
import sys
from itertools import groupby
from nucio import getNucmerAlignmentIterator
from operator import attrgetter
if not len(sys.argv) == 2:
sys.exit("filter_cluster.py in.sc\n")
def edit_distance(in1, in2):
len1 = len(in1)
len2 = len(in2)
mat = [[0]*(len2+1) for _ in range(len1+1)]
#for i in range(0,len1+1):
# mat[i][0] = i
#for j in range(0,len2+1):
# mat[0][j] = j
for i in range(1, len1+1):
for j in range(1,len2+1):
if in1[i-1] == in2[j-1]:
mat[i][j] = mat[i-1][j-1]
else:
mat[i][j] = min( mat[i][j-1], mat[i-1][j], mat[i-1][j-1]) + 1
return mat
def print_matrix(mat):
l1 = len(mat)
for i in range(l1):
print "\t".join(map(lambda x: str(x), mat[i]))
afh = open(sys.argv[1])
alignment_it = getNucmerAlignmentIterator(afh)
for pbname, alignment in groupby(alignment_it, lambda x : x.sname):
print pbname, map(attrgetter("qname"), alignment)
afh.close()