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#!/usr/bin/env python
"""
Add scoring-related parameters to a lastz scores file
-----------------------------------------------------
:Author: Bob Harris (rsharris@bx.psu.edu)
Typical input scores file:
# (a LASTZ scoring set, created by "LASTZ --infer")
bad_score = X:-1910 # used for sub[X][*] and sub[*][X]
fill_score = -191 # used when sub[*][*] not otherwise defined
gap_open_penalty = 400
gap_extend_penalty = 30
A C G T
A 85 -164 -70 -191
C -164 100 -151 -70
G -70 -151 100 -164
T -191 -70 -164 85
"""
import sys
def usage(s=None):
message = """
expand_scores_file [options]< scores_file > scores_file
--overridegaps ignore gap scores already set
"""
if (s == None): sys.exit (message)
else: sys.exit ("%s\n%s" % (s,message))
def main():
overrideGaps = False
for arg in sys.argv[1:]:
if (arg in ["--help","-h","--h","-help"]):
usage()
elif (arg == "--overridegaps"):
overrideGaps = True
continue
usage ("unrecognized argument: %s" % arg)
# read the scores file
lines = []
numValueLines = None
valuesFinished = False
nameToVal = {}
subs = subRows = subColumns = None
lineNumber = 0
for line in sys.stdin:
lineNumber += 1
line = line.rstrip()
lines += [line]
if (line == ""): continue
if (line.startswith("#")): continue
if ("#" in line): line = line.split("#",1)[0].strip()
if ("=" in line):
if (valuesFinished):
raise "in scores file, unexpected assignment (line %d): %s" \
% (lineNumber,line)
fields = line.split("=",1)
name = fields[0].strip()
val = fields[1].strip()
if (name == "gap_open_penalty"): name = "O"
elif (name == "gap_extend_penalty"): name = "E"
if (name in nameToVal):
raise "in scores file, %s is assigned twice (line %d): %s" \
% (name,lineNumber,line)
if (overrideGaps):
if (name in ["O","E"]):
lines.pop()
continue
try:
nameToVal[name] = int_or_float(fields[1])
except:
if (name in ["O","E"]):
raise "in scores file, bad assignment value (line %d): %s" \
% (lineNumber,line)
elif (not valuesFinished):
numValueLines = len(lines) - 1
valuesFinished = True
subColumns = line.split()
subRows = []
subs = {}
else:
fields = line.split()
rowCh = fields.pop(0)
subRows += [rowCh]
if (len(fields) != len(subColumns)):
raise "in scores file, inconsistent matrix (line %d): %s" \
% (lineNumber,line)
for ix in range(len(fields)):
colCh = subColumns[ix]
subs[rowCh+colCh] = int_or_float(fields[ix])
if (subs == None):
raise "scores file is missing a matrix"
if ("AA" not in subs):
raise "scores file lacks A-to-A score"
# compute a few values from the scores matrix
bestSub = float(max([subs[digram] for digram in subs]))
worstSub = float(min([subs[digram] for digram in subs]))
aaSub = float(subs["AA"])
# add expanded values
knownVals = [name for name in nameToVal]
if ("O" not in nameToVal):
nameToVal["O"] = -int(3.25 * worstSub)
if ("E" not in nameToVal):
nameToVal["E"] = -int(0.25 * worstSub)
if ("X" not in nameToVal):
nameToVal["X"] = int(10 * aaSub)
if ("Y" not in nameToVal):
nameToVal["Y"] = int(nameToVal["O"] + 100*nameToVal["E"])
if ("K" not in nameToVal):
nameToVal["K"] = int(30 * bestSub)
if ("L" not in nameToVal):
nameToVal["L"] = int(30 * bestSub)
if ("T" not in nameToVal) and (worstSub/bestSub < -1.5):
nameToVal["T"] = "2"
if ("Z" not in nameToVal) and (worstSub/bestSub < -3.0):
nameToVal["Z"] = "3"
# figure out what values we've added, and in what order to print them
addedNames = [name for name in ["T","Z","O","E","X","Y","K","L"] \
if (name in nameToVal) \
and (name not in knownVals)]
addedNames += [name for name in nameToVal \
if (name not in addedNames) \
and (name not in knownVals)]
# print the new scores file
blankLine = False
for ix in range(numValueLines):
print (lines[ix])
blankLine = (lines[ix] == "")
if (addedNames != []):
if (not blankLine): print ("")
print ("# (score parameters added by expand_scores_file)")
print ("")
for name in addedNames:
print ("%s=%s" % (name,nameToVal[name]))
blankLine = (lines[numValueLines] == "")
if (not blankLine): print ("")
for ix in range(numValueLines,len(lines)):
print (lines[ix])
def int_or_float(s):
try: return int(s)
except: return float(s)
if __name__ == "__main__": main()
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