def doPop(study, force, pop):
setIndivs = study.pops.getIndivs(pop)
hash = MEGA.getHash(setIndivs)
if addPopHash(study.cacheDir + "/pops", pop, hash) or force:
name = "study/%s/%s" % (study.name, pop)
sql.addId(name, hash)
stats.doBasicInfoSet(setIndivs, force)
def doxpEHH(study, force, pop, supp):
logging.info("Starting xpEHH %s %s", pop, supp)
shutil.rmtree("xpEHH", True)
os.mkdir("xpEHH")
os.chdir("xpEHH")
setIndivs = study.getStatIndivs("xpEHH", pop)
suppSetIndivs = study.getStatIndivs("xpEHH", supp)
logging.info("numIndivs: %d %d", len(setIndivs), len(suppSetIndivs))
hash = MEGA.getHash(setIndivs)
hashSupp = MEGA.getHash(suppSetIndivs)
myDir = MEGA.cacheDB + "/sets/" + karyo.karyotype + "/" + hash
logging.info("xpEHH: %s hash: %s phase: %s", pop, hash,
study.getPhasePop("xpEHH", pop))
if not force:
if os.path.isfile(myDir + "/%s-22.uxpEHH" % (supp,)):
logging.info("Already done and not forced")
os.chdir("..")
return
name = "study/%s/xpEHH/%s" % (study.name, pop)
sql.addId(name, hash)
suppName = "study/%s/xpEHH/%s-support" % (study.name, supp)
sql.addId(suppName, hashSupp)
stats.doBasicInfoSet(setIndivs, force)
stats.doBasicInfoSet(suppSetIndivs, force)
w = open(tmpDir + "/xpEHH/inds", "w")
for famId, sampId in setIndivs:
w.write("%s\t%s\n" % (famId, sampId))
w.close()
w = open(tmpDir + "/xpEHH/suppinds", "w")
for famId, sampId in suppSetIndivs:
w.write("%s\t%s\n" % (famId, sampId))
w.close()
os.system("python3 %s/doHaploStats.py prepareData %s %s suppinds %s %s xpEHH" %
(MEGA.haploScripts, karyo.karyotype, study.name,
study.xpEHHConf["source"],
study.getPhasePop("xpEHH", supp)))
for k in range(1, 23 + 1):
shutil.copyfile("%d.hap" % (k,),
"s%d.hap" % (k,))
os.system("python3 %s/doHaploStats.py prepareData %s %s inds %s %s xpEHH" % (
MEGA.haploScripts, karyo.karyotype, study.name,
study.xpEHHConf["source"], study.getPhasePop("xpEHH", pop),))
os.system("python3 %s/doHaploStats.py XPEHH %s" % (
MEGA.haploScripts, karyo.karyotype))
for k in range(1, 23 + 1):
shutil.copyfile("%d.xpEHH" % (k,),
myDir + "/%s-%d.uxpEHH" % (supp, k,))
os.chdir("..")
logging.info("xpEHH Done")
return hash
def doiHS(study, force, pop):
logging.info("Starting iHS")
shutil.rmtree("iHS", True)
os.mkdir("iHS")
os.chdir("iHS")
setIndivs = study.getStatIndivs("iHS", pop)
logging.info("numIndivs: %d", len(setIndivs))
hash = MEGA.getHash(setIndivs)
myDir = MEGA.cacheDB + "/sets/" + karyo.karyotype + "/" + hash
logging.info("iHS: %s hash: %s phase: %s",
pop, hash, study.getPhasePop("iHS", pop))
if not force:
if os.path.isfile(myDir + "/22.uiHS"):
logging.info("Already done and not forced")
os.chdir("..")
return
name = "study/%s/iHS/%s" % (study.name, pop)
sql.addId(name, hash)
stats.doBasicInfoSet(setIndivs, force)
w = open(tmpDir + "/iHS/inds", "w")
for famId, sampId in setIndivs:
w.write("%s\t%s\n" % (famId, sampId))
w.close()
os.system("python3 %s/doHaploStats.py prepareData %s %s inds %s %s" %
(MEGA.haploScripts, karyo.karyotype, study.name,
study.iHSConf["source"], study.getPhasePop("iHS", pop)))
os.system("python3 %s/doHaploStats.py iHS %s %s" % (MEGA.haploScripts,
karyo.karyotype, study.name))
for k in range(1, 23 + 1):
try:
shutil.copyfile("%d.uiHS" % k, myDir + "/%d.uiHS" % k)
except IOError:
pass
os.chdir("..")
logging.info("iHS Done")
return hash
def doPop(pop):
indivs = MEGA.getIndivs(pop)
popHash = stats.doBasicInfoSet(indivs)
sql.addId("pop/" + pop, popHash)