def getStudies(studyDir):
studyLst = os.listdir(studyDir)
studies = {}
for entry in studyLst:
if entry.startswith("."):
continue
studies[entry] = study.getStudy(entry, studyDir)
return studies
fsPair = []
postiHS = set()
postxpEHH = set()
doneIBDs = False
donePCAs = False
doneAdmix = False
doneFs = False
donePlugs = []
for command in commands:
logging.info("command %s", command)
toks = command.split("\t")
if len(toks) < 3:
continue
studyName = toks[0]
if not myStudy or myStudy.name != studyName:
myStudy = study.getStudy(studyName)
mkdir(myStudy.cacheDir)
map_individuals(myStudy)
myStudy.configStudy()
force = toks[1] == "True"
op = toks[2]
if op == "pop":
doPop(myStudy, force, toks[3])
elif op == "IBD":
ibds.append((myStudy, force, toks[3]))
elif op == "IBDEnd":
doneIBDs = True
doIBDs(ibds)
ibds = []
elif op == "pca":
pcas.append((myStudy, force, toks[3]))
import sys
import os
import MEGA
from MEGA import karyo, plink, study
if len(sys.argv) != 4:
print("python %s indlist outfile study")
sys.exit(-1)
lexec = MEGA.executor
indlist = sys.argv[1]
outfile = sys.argv[2]
studyName = sys.argv[3]
s = study.getStudy(studyName)
s.configStudy()
plink.getIndivs(indlist, "tmp" + outfile, lexec=lexec,
acceptFun=karyo.acceptAdmix, suf=s.admix.sampSuff)
lexec.submit("plink", "--silent --noweb --bfile tmp%s --geno %f --mind %f --make-bed --out tmp2%s" %
(outfile, s.admix.minGeno, s.admix.minInd, outfile))
lexec.wait(True)
size, step = karyo.ldTest
lexec.submit("plink", "--silent --noweb --bfile tmp2%s --indep-pairwise %d %d 0.1" % (outfile, size, step))
lexec.wait(True)
if os.path.exists("plink.prune.in"):
lexec.submit("plink", "--silent --noweb --bfile tmp2%s --extract plink.prune.in --make-bed --out %s-auto" % (outfile, outfile))
lexec.wait(True)
os.remove("plink.prune.in")
else:
lexec.submit("plink", "--silent --noweb --bfile tmp2%s --make-bed --out %s-auto" % (outfile, outfile))
import argparse
import os
import MEGA
from MEGA import karyo, plink, study
parser = argparse.ArgumentParser()
parser.add_argument("study", help="Study")
parser.add_argument("indList", help="Individual list (fam, id)")
args = parser.parse_args()
myStudy = study.getStudy(args.study)
myStudy.configStudy()
def ped2eigen(inPref, outPref):
f = open(inPref + ".ped")
iw = open(inPref + ".ind", "w")
snps = {}
for l in f:
toks = l.rstrip().split("\t")
indId = toks[0] + "/" + toks[1]
iw.write(indId + "\tU\tControl\n")
for li in range(len(toks[6:])):
a1, a2 = tuple(toks[li + 6].split(" "))
if a1 not in ["1", "2"] or a2 not in ["1", "2"]:
snps[li] = snps.get(li, "") + "9"
else:
snps[li] = snps.get(li, "") + str(int(a1 == "1") + int(a2 == "1"))
iw.close()
