Practical Bioinformatics: Day 8

aligned1 = "ATTG-GA"
aligned2 = "AT-TGGA"

import monte_aligner

(aligned1,aligned2) = monte_aligner.wormy_step(aligned1,aligned2)
print aligned1
print aligned2

ATTG-GA-
-AT-TGGA

for i in xrange(5):
    (aligned1,aligned2) = monte_aligner.wormy_step(aligned1,aligned2)
    print aligned1
    print aligned2

ATTG-GA--
-AT-TG-GA
ATTGGA--
-A-TTGGA
ATTG-GA-
-A-TTGGA
ATTG-GA
-ATTGGA
ATTG-GA-
--ATTGGA

from gapped import gapped_score, makeIdent

s = makeIdent("ATGC")
s

{'A': {'A': 1, 'C': -1, 'G': -1, 'T': -1},
 'C': {'A': -1, 'C': 1, 'G': -1, 'T': -1},
 'G': {'A': -1, 'C': -1, 'G': 1, 'T': -1},
 'T': {'A': -1, 'C': -1, 'G': -1, 'T': 1}}

for i in xrange(5):
    (aligned1,aligned2) = monte_aligner.wormy_step(aligned1,aligned2)
    print aligned1
    print aligned2
    print gapped_score(aligned1,aligned2,s)

ATTG-G-A
--ATTGGA
-4.0
ATTG-G-A-
--ATTGG-A
-7.0
ATTGG-A-
--ATTGGA
-8.0
ATTGG-A-
--ATTGGA
-8.0
ATTGG-A--
--ATTG-GA
-9.0

import random

random.seed(42)

aligned1 = "ATTG-GA"
aligned2 = "AT-TGGA"

for i in xrange(5):
    (aligned1,aligned2) = monte_aligner.wormy_step(aligned1,aligned2)
    print aligned1
    print aligned2
    print gapped_score(aligned1,aligned2,s)

ATTGGA-
AT-TGGA
-1.0
A-TTGGA
AT-TGGA
3.0
A-TTGGA-
AT-TG-GA
-2.0
A-TTGGA-
AT-TG-GA
-2.0
A-T-TGGA
AT-TG-GA
-2.0

monte_aligner.optimize(aligned1,aligned2,s)

('ATTGGA', 'ATTGGA')