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# Copyright 2003 by Sebastian Bassi. sbassi@genesdigitales.com
# All rights reserved. This code is part of the Biopython
# distribution and governed by its license.
# Please see the LICENSE file that should have been included as part
# of this package.
import math
from string import count
crom=0
compone=[0]
lccsal=[0]
def lcc_mult(seq,wsize,start,end):
"""Return a list called lccsal, the LCC, a complexity measure
from a sequence, called seq."""
l2=math.log(2)
tamseq=end-start
global compone
global lccsal
compone=[0]
lccsal=[0]
for i in range(wsize):
compone.append(((i+1)/float(wsize))*((math.log((i+1)/float(wsize)))/l2))
window=seq[0:wsize]
cant_a=count(window,'A')
cant_c=count(window,'C')
cant_t=count(window,'T')
cant_g=count(window,'G')
term_a=compone[cant_a]
term_c=compone[cant_c]
term_t=compone[cant_t]
term_g=compone[cant_g]
lccsal[0]=(-(term_a+term_c+term_t+term_g))
tail=seq[0]
for x in range (tamseq-wsize):
window=seq[x+1:wsize+x+1]
if tail==window[-1]:
lccsal.append(lccsal[-1])
#break
elif tail=='A':
cant_a=cant_a-1
if window[-1]=='C':
cant_c=cant_c+1
term_a=compone[cant_a]
term_c=compone[cant_c]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif window[-1]=='T':
cant_t=cant_t+1
term_a=compone[cant_a]
term_t=compone[cant_t]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif window[-1]=='G':
cant_g=cant_g+1
term_a=compone[cant_a]
term_g=compone[cant_g]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif tail=='C':
cant_c=cant_c-1
if window[-1]=='A':
cant_a=cant_a+1
term_a=compone[cant_a]
term_c=compone[cant_c]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif window[-1]=='T':
cant_t=cant_t+1
term_c=compone[cant_c]
term_t=compone[cant_t]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif window[-1]=='G':
cant_g=cant_g+1
term_c=compone[cant_c]
term_g=compone[cant_g]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif tail=='T':
cant_t=cant_t-1
if window[-1]=='A':
cant_a=cant_a+1
term_a=compone[cant_a]
term_t=compone[cant_t]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif window[-1]=='C':
cant_c=cant_c+1
term_c=compone[cant_c]
term_t=compone[cant_t]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif window[-1]=='G':
cant_g=cant_g+1
term_t=compone[cant_t]
term_g=compone[cant_g]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif tail=='G':
cant_g=cant_g-1
if window[-1]=='A':
cant_a=cant_a+1
term_a=compone[cant_a]
term_g=compone[cant_g]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif window[-1]=='C':
cant_c=cant_c+1
term_c=compone[cant_c]
term_g=compone[cant_g]
lccsal.append(-(term_a+term_c+term_t+term_g))
elif window[-1]=='T':
cant_t=cant_t+1
term_t=compone[cant_t]
term_g=compone[cant_g]
lccsal.append(-(term_a+term_c+term_t+term_g))
tail=window[0]
return lccsal
def lcc_simp(seq,start,end):
"""Return LCC, a complexity measure from a sequence (seq.)"""
wsize=end-start
l2=math.log(2)
window=seq[start:end]
if count(window,'A')==0:
term_a=0
# This check is usefull in order to avoid calculate log of 0.
else:
term_a=((count(window,'A'))/float(wsize))*((math.log((count(window,'A'))/float(wsize)))/l2)
if count(window,'C')==0:
term_c=0
else:
term_c=((count(window,'C'))/float(wsize))*((math.log((count(window,'C'))/float(wsize)))/l2)
if count(window,'T')==0:
term_t=0
else:
term_t=((count(window,'T'))/float(wsize))*((math.log((count(window,'T'))/float(wsize)))/l2)
if count(window,'G')==0:
term_g=0
else:
term_g=((count(window,'G'))/float(wsize))*((math.log((count(window,'G'))/float(wsize)))/l2)
lccsal=-(term_a+term_c+term_t+term_g)
return lccsal
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