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#!/usr/bin/env python3
"""
Convert probabilities to a LASTZ scores file (including quantum scores)
-----------------------------------------------------------------------
Given background probabilities, probabilities of each DNA substitution event,
and an optional list of quantum symbols, we create a log-odds scoring matrix
suitable for LASTZ.
Typical command line:
probabilities_to_scores --scaleto=100 \
A:.26585 C:.23415 G:.23415 T:.26585 \ <--- background probabilties
AA:.18204 AC:.01903 AG:.04510 AT:.01967 \
CA:.01903 CC:.15508 CG:.01495 CT:.04510 \ <--- substitution probabilties
GA:.04510 GC:.01495 GG:.15508 GT:.01903 \
TA:.01967 TC:.04510 TG:.01903 TT:.18204 \
R=G:.5,A:.5 Y=T:.5,C:.5 <--- quantum symbols
An equivalent command line that takes advantage of the usual symmetry:
probabilities_to_scores --scaleto=100 \
--symmetric \
A:.26585 C:.23415 \ <--- background probabilties
AA:.18204 AC:.01903 AG:.04510 AT:.01967 \ <--- substitution probabilties
CC:.15508 CG:.01495 \
R=G:.5,A:.5 Y=T:.5,C:.5 <--- quantum symbols
The resulting scores file would look like this:
A C G T R Y
A 91 -114 -31 -123 52 -119
C -114 100 -125 -31 -119 52
G -31 -125 100 -114 52 -119
T -123 -31 -114 91 -119 52
R 52 -119 52 -119 52 -119
Y -119 52 -119 52 -119 52
:Author: Bob Harris ([email protected])
"""
import sys
from math import log
def usage(s=None):
message = """
probabilities_to_scores [options] > lastz_score_file
--scaleto=<max> scale scores to give desired max
--symmetric map probabilities symmetrically
--nodna don't include A,G,C,T in the alphabets
--dnarows (target) row alphabet is A,C,G,T
--dnacol[umn]s (query) column alphabet is A,C,G,T
--hoxd70 use HOXD70 (lastz default scores) for probabilities
--iupac alphabets are IUPAC 15-letter code
--writecode=<file> write quantum code to a file
--creator=<string> set name of creator to write as a comment in output
--nocreator inhibit creator comment in output
<base>=<prob> set background probability of a nucleotide
<basepair>=<prob> set basepair substitution probability
<symbol>=<profile> define the profile for a quantum symbol
.. e.g. Y=T:.5,C:.5 or 07=A:0.311,C:0.228,G:0.422,T:0.039
"""
if (s == None): sys.exit (message)
else: sys.exit ("%s\n%s" % (s,message))
bases = "ACGT"
basePairs = ["AA","AC","AG","AT",
"CA","CC","CG","CT",
"GA","GC","GG","GT",
"TA","TC","TG","TT"]
symmetries = [["A","T"],["C","G"],
["AA","TT"],["CC","GG"],["AT","TA"],["CG","GC"],
["AC","CA","GT","TG"],["AG","GA","CT","TC"]]
hoxd70 = [("A", .26585),("C", .23415),
("AA",.18204),("AC",.01903),("AG",.04510),("AT",.01967),
("CC",.15508),("CG",.01495)]
iupac = [("R","G,A"),
("Y","T,C"),
("K","G,T"),
("M","A,C"),
("S","G,C"),
("W","A,T"),
("B","G,T,C"),
("D","G,A,T"),
("H","A,C,T"),
("V","G,C,A"),
("N","A,C,G,T")]
def main():
##########
# parse the command line
##########
prob = {}
scaleTo = None
symmetric = False
dnaQuery = True
symbols = []
symProb = {}
symGroup = {}
settings = []
rowsAreDNA = False
colsAreDNA = False
creator = "probabilities_to_scores"
codeName = None
debug = []
args = sys.argv[1:]
while (len(args) > 0):
arg = args.pop(0)
val = None
fields = arg.split("=",1)
if (len(fields) == 2):
arg = fields[0]
val = fields[1]
if (val == ""):
usage("missing a value in %s=" % arg)
if (arg == "--scaleto") and (val != None):
try: scaleTo = int(val)
except ValueError: scaleTo = float(val)
elif (arg == "--symmetric") and (val == None):
symmetric = True
elif (arg == "--nodna") and (val == None):
dnaQuery = False
elif (arg == "--dnarows") and (val == None):
rowsAreDNA = True
elif (arg in ["--dnacols","--dnacolumns"]) and (val == None):
colsAreDNA = True
elif (arg in ["--hoxd70","--HOXD70"]) and (val == None):
symmetric = True
for (s,p) in hoxd70:
assert (s not in prob), "duplicate DNA event: %s" % s
prob[s] = p
elif (arg in ["--iupac","--IUPAC"]) and (val == None):
for (sym,val) in iupac:
assert (sym not in symProb), "duplicate quantum symbol: %s" % sym
symbols = [sym]
symProb[sym] = {}
symGroup[sym] = ""
vals = val.split(",")
for s in vals:
symProb[sym][s] = 1.0/len(vals)
symGroup[sym] = s
elif (arg == "--writecode") and (val != None):
codeName = val
elif (arg == "--nocreator") and (val == None):
creator = None
elif (arg == "--creator") and (val != None):
creator = val
elif (arg == "--debug") and (val != None):
debug.append(val)
elif (arg == "--debug") and (val == None):
debug.append("debug")
elif (arg.startswith("--")) and (val != None):
settings = [(arg[2:],val)]
elif (arg.startswith("--")):
usage("unknown argument: %s" % arg)
elif (val == None) and (":" in arg):
(s,p) = dna_event(arg)
assert (s not in prob), "duplicate DNA event: %s" % s
prob[s] = p
elif (valid_quantum_symbol(arg)) and (val != None):
sym = arg
assert (sym not in symProb), "duplicate quantum symbol: %s" % sym
symbols = [sym]
symProb[sym] = {}
symGroup[sym] = ""
vals = val.split(",")
haveProbs = False
for val in vals:
if (":" in val):
haveProbs = True
break
if (haveProbs):
for val in vals:
(s,p) = dna_event(val)
assert (len(s) == 1), \
"invalid DNA event for %s: %s" % (sym,s)
assert (s not in symProb[sym]), \
"duplicate DNA event for %s: %s" % (sym,s)
symProb[sym][s] = p
symGroup[sym] = s
else:
for s in vals:
assert (len(s) == 1) and (s in bases), \
"invalid DNA event for %s: %s" % (sym,s)
assert (s not in symProb[sym]), \
"duplicate DNA event for %s: %s" % (sym,s)
symProb[sym][s] = 1.0/len(vals)
symGroup[sym] = s
else:
usage("unknown argument: %s" % arg)
##########
# sanity check
##########
if (symmetric):
for group in symmetries:
present = len([x for x in group if (x in prob)])
assert (present == 1), \
"need a probability for exactly one of %s" \
% (",".join(group))
val = None
for x in group:
if (x in prob):
val = prob[x]
break
for x in group:
if (x not in prob): prob[x] = val
for nuc in bases:
assert (nuc in prob), \
"need a probability for %s" % nuc
for xy in basePairs:
assert (xy in prob), \
"need a probability for %s" % (xy)
p = sum([prob[nuc] for nuc in bases])
assert (abs(p-1) < .000001), \
"base probabilities sum to %f" % p
p = sum([prob[xy] for xy in basePairs])
assert (abs(p-1) < .000001), \
"base pair probabilities sum to %f" % p
for sym in symProb:
p = sum([symProb[sym][nuc] for nuc in symProb[sym]])
assert (abs(p-1) < .000001), \
"probabilities for %s sum to %f" % (sym,p)
for nuc in bases:
if (nuc not in symProb[sym]):
symProb[sym][nuc] = 0
if (dnaQuery):
for sym in bases:
if (sym in symProb): continue
symbols = [sym]
symProb[sym] = {}
symGroup[sym] = sym
for nuc in bases:
if (nuc == sym): symProb[sym][nuc] = 1
else: symProb[sym][nuc] = 0
symbols = [sym for sym in bases] \
[sym for sym in symbols if (sym not in bases)]
if (rowsAreDNA): rowSymbols = bases
else: rowSymbols = symbols
if (colsAreDNA): colSymbols = bases
else: colSymbols = symbols
##########
# print what we got
##########
if ("debug" in debug):
print(" ".join([" %s:%.5f" % (nuc,prob[nuc]) for nuc in bases]))
for x in bases:
print(" ".join(["%s:%.5f" % (x y,prob[x y]) for y in bases]))
print()
for sym in symbols:
p = symProb[sym]
print("%s -> %s" \
% (sym," ".join([" %s:%.5f" % (nuc,p[nuc]) for nuc in bases])))
##########
# write quantum code file
##########
if (codeName != None):
codeF = open(codeName,"wt")
for sym in symbols:
p = symProb[sym]
print("%s\t%s" \
% (sym,"\t".join(["%.6f" % p[nuc] for nuc in bases])), file=codeF)
codeF.close()
##########
# assign scores
##########
sub = {}
maxSub = None
for row in rowSymbols:
u = symProb[row]
sub[row] = {}
for col in colSymbols:
v = symProb[col]
numer = sum([u[y]*v[x]*prob[y x] for (y,x) in basePairs])
denom = sum([u[y]*v[x]*prob[y]*prob[x] for (y,x) in basePairs])
sub[row][col] = log (float(numer) / float(denom))
if (maxSub == None) or (sub[row][col] > maxSub):
maxSub = sub[row][col]
if (scaleTo != None):
scale = scaleTo / maxSub
for row in rowSymbols:
for col in colSymbols:
sub[row][col] *= scale
if (type(scaleTo) == int):
sub[row][col] = round(sub[row][col])
##########
# print the settings, if there are any
##########
if (creator != None):
print("# created by %s" % creator)
print()
if (settings != []):
sLen = max([len(s) for (s,val) in settings])
for (s,val) in settings:
print("%-*s = %s" % (sLen,s,val))
print()
##########
# print the substitution matrix
##########
if (scaleTo != None) and (type(scaleTo) == int):
wSub = 4
for row in rowSymbols:
for col in colSymbols:
wSub = max(wSub,len("%d" % sub[row][col]))
print("%s %s" \
% ("#"," ".join(["%*s" % (wSub,non_single(symGroup[col])) for col in colSymbols])))
print("%s %s" \
% (" "," ".join(["%*s" % (wSub,col) for col in colSymbols])))
for row in rowSymbols:
print("%s %s%s" \
% (row,
" ".join(["%*d" % (wSub,sub[row][col]) for col in colSymbols]),
non_single_comment(symGroup[row])))
else:
wSub = 4
for row in rowSymbols:
for col in colSymbols:
wSub = max(wSub,len("%.6f" % sub[row][col]))
print("%s %s" \
% ("#"," ".join(["%*s" % (wSub,non_single(symGroup[col])) for col in colSymbols])))
print("%s %s" \
% (" "," ".join(["%*s" % (wSub,col) for col in colSymbols])))
for row in rowSymbols:
print("%s %s%s" \
% (row,
" ".join(["%*.6f" % (wSub,sub[row][col]) for col in colSymbols]),
non_single_comment(symGroup[row])))
def dna_event(s):
(s,p) = s.split(":",1)
assert (valid_dna_event(s)), "invalid DNA event: %s" % s
try:
p = float(p)
if (not (0 <= p <= 1)): raise ValueError
except ValueError:
assert (False), "invalid probability for %s: %s" % (s,p)
return (s,p)
def valid_dna_event(s):
if (len(s) == 0):
return False
if (len(s) == 1):
return (s in bases)
if (len(s) == 2):
return (s[0] in bases) and (s[1] in bases)
return False
def valid_quantum_symbol(s):
if (len(s) == 0):
return False
if (len(s) == 1):
return (s in "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789")
if (len(s) == 2):
if (s == "00"): return False
return (s[0] in "0123456789ABCDEF") and (s[1] in "0123456789ABCDEF")
return False
def non_single_comment(s):
if (len(s) == 1): return ""
else: return " # " s
def non_single(s):
if (len(s) == 1): return ""
else: return s
if __name__ == "__main__": main()
|
