def getPopURL(pop, karyo, hash=None, onlyPop=False, onlyKaryo=False):
if not hash:
hash = MEGA.getHash(MEGA.getIndivs(pop))
if onlyPop:
return '<a href="pop.py?md5=%s&k=%s">%s<a>' % (hash, karyo, pop)
elif onlyKaryo:
return '<a href="pop.py?md5=%s&k=%s">%s<a>' % (hash, karyo, karyo)
else:
return '<a href="pop.py?md5=%s&k=%s">%s (%s)<a>' % (hash, karyo, pop, karyo)
def getIndivs(self, pop):
try:
if pop not in self.indsPop:
self.indsPop[pop] = [ind for ind in MEGA.getIndivs(pop)
if ind not in self.alwaysRemove]
for addPop in self.addPops.get(pop, []):
popInds = MEGA.getIndivs(addPop)
self.indsPop[pop].extend([ind for ind in popInds
if ind not in self.alwaysRemove])
for i, ind in enumerate(self.addInds.get(pop, [])):
if ind not in self.alwaysRemove:
self.indsPop[pop].append(ind)
for ind in self.delInds.get(pop, []):
self.indsPop[pop].remove(ind)
except ValueError:
logging.error("pop getIndivs %s %s %s" % (
self.study.name, pop, ind))
return self.indsPop[pop]
def doBundle(bundle, pops, sizes):
myIndivs = []
for i in range(len(pops)-1):
myIndivs.extend(MEGA.getIndivs(pops[i]))
doPop(pops[i], sizes[i], MEGA.getIndivs(pops[i]))
try:
os.mkdir(os.sep.join([MEGA.cacheDB, "bundles"]))
except OSError:
pass #Already exists, OK
bundleDir = os.sep.join([MEGA.cacheDB, "bundles", pop])
try:
os.mkdir(bundleDir)
except OSError:
pass #Already exists, OK
w = open(bundleDir + os.sep + "basic", "w")
w.write(str(sizes[-1]) + "\n")
for i in range(len(pops)-1):
w.write("\t".join([pops[i], str(sizes[i])]))
w.write("\n")
w.close()
w = open(bundleDir + os.sep + "indivs", "w")
w.write("\n".join(map(lambda x:str(x), myIndivs)) + "\n")
w.close()
def doBundle(bundle, pops, sizes):
myIndivs = []
for i in range(len(pops) - 1):
myIndivs.extend(MEGA.getIndivs(pops[i]))
doPop(pops[i], sizes[i], MEGA.getIndivs(pops[i]))
try:
os.mkdir(os.sep.join([MEGA.cacheDB, "bundles"]))
except OSError:
pass #Already exists, OK
bundleDir = os.sep.join([MEGA.cacheDB, "bundles", pop])
try:
os.mkdir(bundleDir)
except OSError:
pass #Already exists, OK
w = open(bundleDir + os.sep + "basic", "w")
w.write(str(sizes[-1]) + "\n")
for i in range(len(pops) - 1):
w.write("\t".join([pops[i], str(sizes[i])]))
w.write("\n")
w.close()
w = open(bundleDir + os.sep + "indivs", "w")
w.write("\n".join(map(lambda x: str(x), myIndivs)) + "\n")
w.close()
import sys
import MEGA
if len(sys.argv)!=2:
print "python %s pop" % (sys.argv[0],)
sys.exit(-1)
pop=sys.argv[1]
if pop in MEGA.bundles:
print "BUNDLE"
myPops = MEGA.bundles[pop]
cnt = 0
for myPop in myPops:
myLen = len(MEGA.getIndivs(myPop))
print "%20s\t%5d" % (myPop, myLen)
cnt += myLen
print "%20s\t%5d" %("All", cnt)
else:
print "CORE POP"
print len(MEGA.getIndivs(pop))
except OSError:
pass #Already exists, OK
bundleDir = os.sep.join([MEGA.cacheDB, "bundles", pop])
try:
os.mkdir(bundleDir)
except OSError:
pass #Already exists, OK
w = open(bundleDir + os.sep + "basic", "w")
w.write(str(sizes[-1]) + "\n")
for i in range(len(pops)-1):
w.write("\t".join([pops[i], str(sizes[i])]))
w.write("\n")
w.close()
w = open(bundleDir + os.sep + "indivs", "w")
w.write("\n".join(map(lambda x:str(x), myIndivs)) + "\n")
w.close()
if len(lines)==2: #CORE POP
size = int(lines[1])
doPop(pop, size, MEGA.getIndivs(pop))
else:
pops = []
sizes = []
for line in lines[1:]:
toks = line.rstrip().split("\t")
pops.append(toks[0].lstrip().rstrip())
sizes.append(int(toks[1]))
doBundle(pop, pops, sizes)
for path in paths:
sys.path.insert(0, os.path.expanduser(path))
import MEGA
from MEGA import web
web.sendPreamble(None, None, "Populations")
print("<h2>Populations</h2>")
pops = MEGA.pops
karyos = os.listdir(MEGA.cacheDB + "/sets/")
print('<table border="1">')
curr = 1
print("<tr>")
for pop in pops:
indivs = MEGA.getIndivs(pop)
hash = MEGA.getHash(indivs)
print('<td>')
print(pop)
start = False
for myKaryo in karyos:
if os.path.isdir('%s/sets/%s/%s' % (MEGA.cacheDB, myKaryo, hash)):
print("%s" % web.getPopURL(pop, myKaryo, hash, onlyKaryo=True))
print('</td>')
if curr % 6 == 0:
print("</tr><tr>")
curr += 1
print("</tr>")
print("</table>")
os.mkdir(os.sep.join([MEGA.cacheDB, "bundles"]))
except OSError:
pass #Already exists, OK
bundleDir = os.sep.join([MEGA.cacheDB, "bundles", pop])
try:
os.mkdir(bundleDir)
except OSError:
pass #Already exists, OK
w = open(bundleDir + os.sep + "basic", "w")
w.write(str(sizes[-1]) + "\n")
for i in range(len(pops) - 1):
w.write("\t".join([pops[i], str(sizes[i])]))
w.write("\n")
w.close()
w = open(bundleDir + os.sep + "indivs", "w")
w.write("\n".join(map(lambda x: str(x), myIndivs)) + "\n")
w.close()
if len(lines) == 2: #CORE POP
size = int(lines[1])
doPop(pop, size, MEGA.getIndivs(pop))
else:
pops = []
sizes = []
for line in lines[1:]:
toks = line.rstrip().split("\t")
pops.append(toks[0].lstrip().rstrip())
sizes.append(int(toks[1]))
doBundle(pop, pops, sizes)
def doPop(pop):
indivs = MEGA.getIndivs(pop)
popHash = stats.doBasicInfoSet(indivs)
sql.addId("pop/" + pop, popHash)
