def getAll(self):
w = open("indlist", "w")
for pop in self.study.pops.pops:
for fam, ind in self.study.pops.getIndivs(pop):
w.write("%s\t%s\n" % (fam, ind))
w.close()
acceptFun = eval("karyo." + self.acceptFun)
plink.getIndivs("indlist", "plink", acceptFun=acceptFun,
suf=self.sampSuff)
def getPerPop(self):
acceptFun = eval("karyo." + self.acceptFun)
for i, pop in enumerate(self.pops):
#we do not use pop name as a suffix because of spaces, using i
w = open('indlist-%d' % i, 'w')
all_pops = pop.split('+')
for pop_ in all_pops:
for fam, ind in self.study.pops.getIndivs(pop_):
w.write("%s\t%s\n" % (fam, ind))
w.close()
plink.getIndivs("indlist-%d" % i, "plink-%d" % i,
lexec=MEGA.executor,
acceptFun=acceptFun, suf=self.sampSuff)
MEGA.executor.wait(True)
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))
lexec.wait(True)
rmfs = os.listdir(".")
for rmf in rmfs:
if chro == "23" and not has19:
chro = "19"
# This is a ridiculous hack to make smartpca work on X
sw.write("%s\t%s\t0.0\t%s\n" % (toks[1], chro, toks[3]))
sw.close()
f.close()
gw = open(inPref + ".eigenstratgeno", "w")
poses = list(snps.keys())
poses.sort()
for pos in poses:
gw.write(snps[pos] + "\n")
gw.close()
f.close()
f.close()
lexec = MEGA.executor
lexec.mem = 5000 * karyo.memMult
plink.getIndivs(args.indList, "pca", lexec, acceptFun=karyo.acceptAdmix,
suf=myStudy.pca.sampSuff)
os.system("plink --silent --noweb --bfile pca --geno 0.1 --maf %f --make-bed --out pca2" %
myStudy.pca.MAF)
size, step = karyo.ldTest
os.system("plink --silent --bfile pca2 --indep-pairwise %d %d 0.1 --out SNPStoBeKept --noweb" % (size, step))
os.system("plink --silent --bfile pca2 --extract SNPStoBeKept.prune.in --noweb --recode12 --tab --out pca2")
ped2eigen("pca2", "pca2")
os.system("smartpca.perl -i pca2.eigenstratgeno -a pca2.snp -b pca2.ind -o expl -p plt -e evl -l log -m 0")
if cnt > 0:
end = pos
write_block(block, chro, start, end)
block += 1
return block
if args.step == "prepFST":
group = args.group
try:
os.mkdir(group)
except OSError:
pass
os.chdir(group)
os.system('rm gp-* 2>/dev/null')
plink.getIndivs("../" + indList, "fst", isBinary=False,
acceptFun=lambda chro, pos: chro == karyo.groups[group]
and karyo.accept(chro, pos), suf=myStudy.fs.sampSuff)
os.system("plink --noweb --recode --file fst --maf %f --out gp" %
myStudy.fs.MAF)
nblocks = slice_plink("gp", args.max)
for block in range(nblocks):
to_genepop("gp-%d" % block, "conv-%d" % block, popList)
elif args.step == "FST":
group = args.group
os.chdir(group)
for i in range(100000):
try:
os.mkdir(str(i))
except OSError:
pass
if os.path.exists("conv-%d.gp" % i):
