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estimate-dispersion.py
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estimate-dispersion.py
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#!/usr/bin/env python
#=========================================================================
# This is OPEN SOURCE SOFTWARE governed by the Gnu General Public
# License (GPL) version 3, as described at www.opensource.org.
# Copyright (C)2018 William H. Majoros (bmajoros@alumni.duke.edu)
#=========================================================================
from __future__ import (absolute_import, division, print_function,
unicode_literals, generators, nested_scopes, with_statement)
from builtins import (bytes, dict, int, list, object, range, str, ascii,
chr, hex, input, next, oct, open, pow, round, super, filter, map, zip)
# The above imports should allow this program to run in both Python 2 and
# Python 3. You might need to update your version of module "future".
import sys
import os
import math
import ProgramName
from Rex import Rex
rex=Rex()
import TempFilename
import getopt
from StanParser import StanParser
from PooledParser import PooledParser
from Stan import Stan
DEBUG=False
MU=1 # mean of lognormal prior on ratio RNA/DNA
SIGMA=3 # std dev of lognormal prior on ratio RNA/DNA
WARMUP=1000
ALPHA=0.05
STDERR=TempFilename.generate(".stderr")
INPUT_FILE=TempFilename.generate(".staninputs")
INIT_FILE=TempFilename.generate(".staninit")
OUTPUT_TEMP=TempFilename.generate(".stanoutputs")
def printFields(fields,hFile):
numFields=len(fields)
for i in range(7,numFields):
print(i-6,"=",fields[i],sep="",end="",file=hFile)
if(i<numFields-1): print("\t",end="",file=hFile)
print(file=hFile)
def getFieldIndex(label,fields):
numFields=len(fields)
index=None
for i in range(7,numFields):
if(fields[i]==label): index=i
return index
def writeToFile(fields,OUT):
numFields=len(fields)
for i in range(7,numFields):
print(fields[i],end="",file=OUT)
if(i<numFields-1): print("\t",end="",file=OUT)
print(file=OUT)
def writeInitializationFile(stan,variant,filename):
OUT=open(filename,"wt")
numPools=variant.numPools()
print("d <- 100",file=OUT)
print("r_ref <- 1",file=OUT)
print("r_alt <- 1",file=OUT)
OUT.close()
def writePoolTypes(stan,variant,OUT):
poolTypes=[]
for pool in variant.pools:
poolTypes.append(pool.getPoolType())
stan.writeOneDimArray("POOL_TYPE",poolTypes,len(poolTypes),OUT)
def writeInputsFile(stan,variant,filename):
OUT=open(filename,"wt")
numPools=variant.numPools()
print("N_POOLS <-",numPools,file=OUT)
print("mu <-",MU,file=OUT)
print("sigma2 <-",SIGMA*SIGMA,file=OUT)
writePoolTypes(stan,variant,OUT)
dnaAltCounts=[pool.DNA[0].alt for pool in variant.pools]
dnaRefCounts=[pool.DNA[0].ref for pool in variant.pools]
rnaAltCounts=[pool.RNA[0].alt for pool in variant.pools]
rnaRefCounts=[pool.RNA[0].ref for pool in variant.pools]
stan.writeOneDimArray("a",dnaAltCounts,numPools,OUT)
stan.writeOneDimArray("b",dnaRefCounts,numPools,OUT)
stan.writeOneDimArray("k",rnaAltCounts,numPools,OUT)
stan.writeOneDimArray("m",rnaRefCounts,numPools,OUT)
OUT.close()
def runVariant(stan,variant,numSamples,outfile):
# Write inputs file for STAN
writeInputsFile(stan,variant,INPUT_FILE)
writeInitializationFile(stan,variant,INIT_FILE)
# Run STAN model
cmd=stan.getCmd(WARMUP,numSamples,INPUT_FILE,OUTPUT_TEMP,STDERR,INIT_FILE)
if(DEBUG):
print(cmd)
exit()
os.system(cmd)
# Parse MCMC output
parser=StanParser(OUTPUT_TEMP)
conc=parser.getVariable("d")
return (conc,parser)
#def summarize(parser,conc,ID,minRight):
# (median,CI_left,CI_right)=parser.getMedianAndCI(1.0-ALPHA,"conc")
# maxLeft=1.0/minRight
# leftP=parser.getLeftTail("theta",maxLeft)
# rightP=parser.getRightTail("theta",minRight)
# Preg=leftP if leftP>rightP else rightP
# print(ID,median,CI_left,CI_right,Preg,sep="\t")
#=========================================================================
# main()
#=========================================================================
(options,args)=getopt.getopt(sys.argv[1:],"s:t:")
if(len(args)!=5):
exit(ProgramName.get()+" [-s stanfile] <model> <input.essex> <output.txt> <#MCMC-samples> <firstVariant-lastVariant>\n -s = save raw STAN file\n\n variant range is zero-based and inclusive\n")
(model,inFile,outfile,numSamples,numVariants)=args
stanFile=None
for pair in options:
(key,value)=pair
if(key=="-s"): stanFile=value
if(not rex.find(r"(\d+)-(\d+)",numVariants)):
exit(numVariants+": specify range of variants: first-last")
firstIndex=int(rex[1])
lastIndex=int(rex[2])
stan=Stan(model)
# Process all input lines, each line = one variant (one MCMC run)
variantIndex=0
pooledParser=PooledParser(inFile)
while(True):
variant=pooledParser.nextVariant()
if(variant is None): break
# Check whether this variant is in the range to be processed
if(variantIndex<firstIndex):
variantIndex+=1
continue
elif(variantIndex>lastIndex): break
variant.collapseReplicates()
(dispersion,stanParser)=runVariant(stan,variant,numSamples,outfile)
if(dispersion is None): continue
(median,CI_left,CI_right)=stanParser.getMedianAndCI(1.0-ALPHA,"d")
print(variant.ID,median,sep="\t")
variantIndex+=1
os.remove(STDERR)
os.remove(INPUT_FILE)
if(stanFile is None):
os.remove(OUTPUT_TEMP)
else:
os.system("cp "+OUTPUT_TEMP+" "+stanFile)