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####################################################################
# combine_replicates.py
# used to combine lamarc runs from multiple replicates into a
# single region file with insumfiles for "poor man's parallelization"
####################################################################
# system imports
import getopt
import random
import re
import sys
import os.path
from xml.dom.minidom import parse, Document
import parallelCommon
file_reg_rep_pattern = re.compile('reg(.*)_rep(.*)')
number_pattern = re.compile('\s*(\d+)\s+(\d+)\s+(\d+)')
reg_rep_pattern = re.compile('\s*(\d+)\s+(\d+)')
# each file assumes it is for the only region and only replicate
# and so has region and replicate numbers of zero. Here we
# replace those zeroes in the <number> and <reg_rep> tags
def replaceReplicateNumbers(myElem,repNum):
if repNum < 0:
print "bad replicate number, %s , to replaceReplicateNumbers\n" , repNum
exit(2)
for numberTag in myElem.getElementsByTagName("number"):
for child in numberTag.childNodes:
if child.nodeType == child.TEXT_NODE:
m = number_pattern.match(child.data)
if m:
child.data = " %s %s %s " % (m.group(1),repNum,m.group(3))
for regRepTag in myElem.getElementsByTagName("reg_rep"):
for child in regRepTag.childNodes:
if child.nodeType == child.TEXT_NODE:
m = reg_rep_pattern.match(child.data)
if m:
child.data = " %s %s " % (m.group(1),repNum)
# combine outsumfiles for multiple replicates over a single region
# into a single insumfile.
# argument "regString" will usually be something like "reg2", but
# can be "final" for a multiple replicate run over a single region
def combineSumfiles(lamdir,regString,regRepList):
parallelCommon.sumfileCombineWarn(regString)
# create output dom
sumDoc = Document()
topElem = sumDoc.createElement("XML-summary-file")
sumDoc.appendChild(topElem)
for suffix in regRepList:
# get reg and rep number form suffix
m = file_reg_rep_pattern.match(suffix)
regNum = ""
repNum = ""
if m:
regNum = m.group(1)
repNum = m.group(2)
# find file and parse it in
outsumdir = os.path.join(lamdir,'%s' % suffix)
oneRep = os.path.join(outsumdir,'outsumfile_%s.xml' % suffix)
inf = open(oneRep,'r')
oneDom = parse(inf)
inf.close()
localTop = parallelCommon.getFirstTag(oneDom,"XML-summary-file")
# add to output xml structure
childNodeList = localTop.childNodes
for myNode in childNodeList:
myNewNode = sumDoc.importNode(myNode,True)
topElem.appendChild(myNewNode)
if myNewNode.nodeType == myNewNode.ELEMENT_NODE:
replaceReplicateNumbers(myNewNode,repNum)
# write output file
insumdir = os.path.join(lamdir,'%s' % regString)
sumfile = os.path.join(insumdir,'insumfile_%s.xml' % regString)
outf = open(sumfile,'w')
sumDoc.writexml(outf)
outf.close()
parallelCommon.stripXmlInfo(sumfile)
# input options
[lamarcfile,lamdir,pydir] = parallelCommon.getOptionsAndVerify(False)
parallelCommon.describeThisScript("combine_replicates.py","combine replicate runs for each region",lamarcfile,lamdir)
inlamarc = open(lamarcfile,'r')
lamDom = parse(inlamarc)
inlamarc.close()
# add comment to identify outfile as generated by this script
lamarcTag = parallelCommon.getFirstTag(lamDom,"lamarc")
commentNode = lamDom.createComment("Created by combine_replicates.py")
lamarcTag.insertBefore(commentNode,lamarcTag.firstChild)
# divide up regions
dataElem = parallelCommon.getSingleTag(lamarcTag,"data")
regionElems = dataElem.getElementsByTagName("region")
singleRegion = len(regionElems) == 1
# turn off profiling -- we only do it at the end
if not singleRegion:
parallelCommon.turnProfilesOff(lamDom,lamarcTag)
# find replicate number -- do not change it
chainsTag = parallelCommon.getFirstTag(lamarcTag,"chains")
replicatesTag = parallelCommon.getFirstTag(chainsTag,"replicates")
originalReplicateCount = 1
if replicatesTag:
originalReplicateCount = parallelCommon.getLongVal(replicatesTag)
# find format tag
formatTag = parallelCommon.getFirstTag(lamarcTag,"format")
# disconnect regions from dom
for region in regionElems:
dataElem.removeChild(region)
infileList = []
# output each region file
regCount = 0
for region in regionElems:
dataElem.appendChild(region)
repList = []
for repCount in range(originalReplicateCount):
idString = 'reg%d_rep%d' % (regCount,repCount)
repList.append(idString)
regString = 'reg%d' % regCount
if singleRegion:
regString = "final"
parallelCommon.fixFormatTag(lamDom,formatTag,regString,True)
runDir = os.path.join(lamdir,'%s' % regString)
if not os.path.exists(runDir):
os.makedirs(runDir)
regFile = os.path.join(runDir,'infile_%s.xml' % regString)
outf = open(regFile,'w')
lamDom.writexml(outf)
outf.close()
infileList.append(regFile)
combineSumfiles(lamdir,regString,repList)
dataElem.removeChild(region)
regCount = regCount + 1
# unlink region
# output instructions: files to run, next program to run
parallelCommon.nextStep(lamdir,infileList,singleRegion)
if not singleRegion:
parallelCommon.finalStep(pydir,"combine_regions.py",lamarcfile,lamdir)
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