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####################################################################
# combine_regions.py
# used to combine lamarc runs from regions (which may include
# multiple replicates) into a single region file with insumfiles
# for "poor man's parallelization"
####################################################################
# system imports
import re
import os.path
import sys
from xml.dom.minidom import parse, Document
import parallelCommon
file_reg_pattern = re.compile('reg(.*)')
number_pattern = re.compile('\s*(\d+)\s+(\d+)\s+(\d+)')
reg_rep_pattern = re.compile('\s*(\d+)\s+(\d+)')
t_number_pattern = re.compile('(\s*<number>\s*)(\d+)(\s+\d+\s+\d+\s*</number>\s*)')
t_reg_rep_pattern = re.compile('(\s*<reg_rep>\s*)(\d+)(\s+\d+\s*</reg_rep>\s*)')
t_top_tag_pattern = re.compile('.*XML.summary.file.*')
# each file assumes it is for the only region
# and so has region numbers of zero. Here we
# replace those zeroes in the <number> and <reg_rep> tags
def replaceRegionNumbers(myElem,regNum):
if regNum < 0:
print "Bad region number, %s, to replaceRegionNumbers\n" , regNum
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 " % (regNum,m.group(2),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 " % (regNum,m.group(2))
# combine outsumfiles for single regions into a single insumfile.
#
# lamdir == top level directory containing subdirectories for runs
# rundir == where to write the sumfile
# regionList == list of strings like "reg0" and "reg1"
def combineSumfilesRegion(lamdir,rundir,regionList):
parallelCommon.sumfileCombineWarn(rundir)
# write output file
sumfile = os.path.join(rundir,'insumfile_final.xml')
outf = open(sumfile,'w')
outf.write("<XML-summary-file>\n")
for suffix in regionList:
# get reg and rep number form suffix
m = file_reg_pattern.match(suffix)
regNum = ""
if m:
regNum = m.group(1)
# find file and parse it in
sumdir = os.path.join(lamdir,'reg%s' % regNum)
oneRep = os.path.join(sumdir,'outsumfile_%s.xml' % suffix)
print "processing %s" % oneRep
sys.stdout.flush()
# append to existing file, changing region numbers as necessary
for line in open(oneRep):
# throw away outermost tags
m = t_top_tag_pattern.match(line)
if m:
continue
# replace region number in <number> tag and continue
m = t_number_pattern.match(line)
if m:
outf.write("%s%s%s\n" % (m.group(1),regNum,m.group(3)))
continue
# replace region number in <reg_rep> tag and continue
m = t_reg_rep_pattern.match(line)
if m:
outf.write("%s%s%s\n" % (m.group(1),regNum,m.group(3)))
continue
# not a special case
outf.write("%s\n" % line)
outf.write("</XML-summary-file>\n")
outf.close()
def combineSumfilesRegion__OLD(lamdir,rundir,regionList):
parallelCommon.sumfileCombineWarn(rundir)
# create output dom
sumDoc = Document()
topElem = sumDoc.createElement("XML-summary-file")
sumDoc.appendChild(topElem)
for suffix in regionList:
# get reg and rep number form suffix
m = file_reg_pattern.match(suffix)
regNum = ""
if m:
regNum = m.group(1)
# find file and parse it in
sumdir = os.path.join(lamdir,'reg%s' % regNum)
oneRep = os.path.join(sumdir,'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:
replaceRegionNumbers(myNewNode,regNum)
# write output file
sumfile = os.path.join(rundir,'insumfile_final.xml')
outf = open(sumfile,'w')
sumDoc.writexml(outf)
outf.close()
parallelCommon.stripXmlInfo(sumfile)
# input options
[lamarcfile,lamdir,pydir] = parallelCommon.getOptionsAndVerify(False)
parallelCommon.describeThisScript("combine_regions","combine all regions and replicates",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_regions.py")
lamarcTag.insertBefore(commentNode,lamarcTag.firstChild)
# EWFIX.REMOVE
# 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")
# divide up regions
dataElem = parallelCommon.getSingleTag(lamarcTag,"data")
regionElems = dataElem.getElementsByTagName("region")
infileList = []
# output each region file
regionList = []
for regCount in range(regionElems.length):
idString = 'reg%d' % regCount
regionList.append(idString)
parallelCommon.fixFormatTag(lamDom,formatTag,"final",True)
rundir = os.path.join(lamdir,'final')
os.makedirs(rundir)
regFile = os.path.join(rundir,'infile_final.xml')
outf = open(regFile,'w')
lamDom.writexml(outf)
outf.close()
combineSumfilesRegion(lamdir,rundir,regionList)
# output instructions: files to run, next program to run
parallelCommon.nextStep(lamdir,[regFile],True)
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