Solution for this thread: http://forum.ubuntuusers.de/topic/programmieraufgabe-wie-loesbar/

count_triples.py

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

import sys
import argparse
from contextlib import closing

import io


def count_triples_seahawk1986(sequences):
    """
    Ansatz von Seahawk1986: http://forum.ubuntuusers.de/post/4689377/
    (just ported to Python3 with `io`-Module)
    """
    line1 = io.StringIO()
    line2 = io.StringIO()

    a, b = sequences
    
    line1.write("".join(a))
    line2.write("".join(b))

    line1.seek(0)
    line2.seek(0)

    
    result1 = io.StringIO()
    result2 = io.StringIO()
    pos = 0
    lenstr = len(line1.getvalue()) - 3
    line1.seek(0)
    line2.seek(0)
    while pos <= lenstr:
        trip1 = line1.read(3)
        trip2 = line2.read(3)
        if trip1.isalpha() and trip2.isalpha():
            result1.write(trip1)
        pos +=3
    return int(len(result1.getvalue()) / 3)


def count_triples_seahawk1986_2(sequences):
    """
    Ansatz von Seahawk1986: http://forum.ubuntuusers.de/post/4689377/
    (just ported to Python3 with `io`-Module)
    
    Umgestellt auf das Testen auf Gaps "-" analog zu `count_triples2`
    """
    line1 = io.StringIO()
    line2 = io.StringIO()

    a, b = sequences
    
    line1.write("".join(a))
    line2.write("".join(b))

    line1.seek(0)
    line2.seek(0)

    
    result1 = io.StringIO()
    result2 = io.StringIO()
    pos = 0
    lenstr = len(line1.getvalue()) - 3
    line1.seek(0)
    line2.seek(0)
    while pos <= lenstr:
        trip1 = line1.read(3)
        trip2 = line2.read(3)
        if "-" not in trip1 and "-" not in trip2:
            result1.write(trip1)
        pos +=3
    return int(len(result1.getvalue()) / 3)


def is_gap(a, b):
    return a.isalpha() and b.isalpha()
          

def count_triples1(sequences):
    return int(sum(1 for a, b in zip(*sequences) if is_gap(a, b)) / 3)


def count_triples2(sequences):
    return int(sum(1 for pair in zip(*sequences) if "-" not in pair) / 3)


def load(f):
    with closing(f):
        for line in f:
            line = line.strip()
            if line:
                yield line


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="search gap free dna blocks")
    parser.add_argument("-algo", default="lys2",
                        choices=("lys1", "lys2", "sea1", "sea2"),
                        help="choose algorithm: %(choices)s "
                             "(default: %(default)s)")
    parser.add_argument("dnafiles", nargs=2, type=argparse.FileType("r"), 
                        default=sys.stdin)
    
    args = parser.parse_args()
    dnafiles = map(load, args.dnafiles)
    
    print({
        "lys1": count_triples1,
        "lys2": count_triples2,
        "sea1": count_triples_seahawk1986,
        "sea2": count_triples_seahawk1986_2
    }[args.algo](dnafiles))

measure.py

#!/usr/bin/env python

import argparse
import sys
from count_triples import load, count_triples1, count_triples2, \
                          count_triples_seahawk1986, count_triples_seahawk1986_2


def main():
    parser = argparse.ArgumentParser(description="search gap free dna blocks")
    parser.add_argument("dnafiles", nargs=2, type=argparse.FileType("r"), 
                        default=sys.stdin)
    
    args = parser.parse_args()
    dnafiles = map(load, args.dnafiles)
    # we need data for multiple usage
    sequences = ["".join(s) for s in dnafiles]

    import timeit

    for func in [count_triples1, count_triples2, count_triples_seahawk1986,
                 count_triples_seahawk1986_2]:
        t = timeit.Timer("{0}({1})".format(func.__name__, sequences),
                         "from __main__ import {0}".format(func.__name__))
        count = 1000
        print(func.__name__, (t.timeit(count) / count))


if __name__ == "__main__":
    main()