Question

I have two sets of lists that are synchronized and look like this:
(by synchronized I mean that ‘A’ in cal belongs to 12 in cpos, and ‘A’ in mal belongs to 11 in mpos)

set1

cpos = [12, 13, 14, 15]
cal = ['A', 'T', 'C', 'G']

set2

mpos = [11, 12, 13, 16]
mal = ['A', 'T', 'T', 'G']

I want to find a match between the two sets, and in this example there is only one match, 13T in cpos&cal and 13T in mpos&mal.

I wrote this script, but it only compares the values by indices it seems, since the match string is empty:

mat = []
for i in xrange(len(cpos)):
     if mpos[i] == cpos[i] and mal[i] == cal[i]:
             mat.append(cpos[i])

This is what I wanted to get:

mat = [13]

Any ideas how to solve this?

Answer 1

cpos = [12, 13, 14, 15]
cal = ['A', 'T', 'C', 'G']

mpos = [11, 12, 13, 16]
mal = ['A', 'T', 'T', 'G']

set1 = set(zip(cpos, cal))
set2 = set(zip(mpos, mal))

print set1 & set2

Result:

## set([(13, 'T')])

As per @Janne Karila’s comments below, the following will be more efficient:

from itertools import izip
print set(izip(cpos, cal)).intersection(izip(mpos, mal))

Timings:

import timeit

repeat = 1

setup = '''
num = 1000000
import random
import string
from itertools import izip
cpos = [random.randint(1, 100) for x in range(num)]
cal = [random.choice(string.letters) for x in range(num)]
mpos = [random.randint(1, 100) for x in range(num)]
mal = [random.choice(string.letters) for x in range(num)]
'''

# izip: 0.38 seconds (Python 2.7.2)
t = timeit.Timer(
     setup = setup,
     stmt = '''set(izip(cpos, cal)).intersection(izip(mpos, mal))'''
)

print "%.2f second" % (t.timeit(number=repeat))



# zip: 0.53 seconds (Python 2.7.2)
t = timeit.Timer(
     setup = setup,
     stmt = '''set(zip(cpos, cal)) & set(zip(mpos, mal))'''
)

print "%.2f second" % (t.timeit(number=repeat))


# Nested loop: 616 seconds (Python 2.7.2)
t = timeit.Timer(
     setup = setup,
     stmt = '''

mat = []
for i in xrange(len(cpos)):
     for j in xrange(len(mpos)):
          if mpos[j] == cpos[i] and mal[j] == cal[i]:
               mat.append(mpos[j]) # or mat.append((mpos[j], mal[j])) ?
               break
'''
)

print "%.2f seconds" % (t.timeit(number=repeat))