idStr = id[0]
if idStr.find("xpEHH"):
toks = idStr.split("/")
myStudies.append(toks[1] + "/" + toks[-1])
web.sendPreamble(md5, None, "xpEHH")
os.chdir(xpehhPath)
print('<a href="pop.py?md5=%s">Population page</a>' % (md5,))
print("<h1>xpEHH</h1>")
print(",".join(myStudies))
print("<h2>Bulk Downloads</h2>(support %s)<br>" % sPop)
fNames = os.listdir(".")
print(web.linkFile((karyo, md5), "%s-uxpEHH.zip" % sPopURL, "Download bulk data (unstandardized)",))
print(web.linkFile((karyo, md5), "%s-xpEHH.zip" % sPopURL, "Download bulk data (standardized)",))
print(web.linkFile((karyo, md5), "xpEHH-%s.window" % sPopURL, "Download bulk data (Window)",))
cwd = os.getcwd()
os.chdir(MEGA.cacheDB + "/sets/" + karyo + '/' + md5)
print("<h2>Mean, standard deviation</h2>")
try:
f = open(xpehhPath + "/xpEHH-" + sPop + ".stats")
print((", ".join(f.readlines())))
f.close()
#print '<br><img src="/cgi-bin/xpEHH.py?md5=%s&op=png">'% (hash,)
except IOError:
print("Not available")
print('</tr>')
for pop in study.pops.pops:
md5 = MEGA.getHash(study.pops.getIndivs(pop))
print("<tr>")
print("<td>", web.getPopURL(pop, karyo.karyotype, md5), "</td>")
print("<td>", len(study.pops.getIndivs(pop)), "</td>")
for cut in cuts:
try:
print('<td>', len(study.ibd.getIndivsPop(pop, cut)), '</td>')
except IOError:
print('<td></td>')
print("</tr>")
print("</td>")
print("</tr></table>")
print("<br>")
print(web.linkFile(studyName, "ibd.problems", "IBD issues (>12.5)", True))
print('<h2>PCA</h2>')
print('<table border=1>')
for i in range(study.pca.numPCAs):
print('<tr>')
print('<td>')
print(web.linkFile(studyName, 'pca%d.evec' % i, 'PCA Matrix', True))
print(web.linkFile(studyName, 'pca%d.evl' % i, 'PCA weights', True))
print('</td><td>')
print(web.linkFile(studyName, 'pca%d.png' % i,
None, True, True, attrs='width="1000"'))
print("</td>")
print("</tr>")
print("</table>")
print("<h2>Admixture</h2>")
popName = popInfo[0]
if len(popInfo)>1:
suppPop = popInfo[1]
header.append(popName + "/" + suppPop)
else:
header.append(popName)
header.extend(["Top", "1%", "Top+1%", "5%"])
def outFun(toks):
toks[1] = '<a href="%s/gtf.py?k=%d&start=%d&end=%d">%s</a>' % (
MEGA.webRoot,
int(toks[0]), int(toks[1]), int(toks[1])+200000, toks[1])
return toks
web.table("comparison.py", cgi, "cmp.top.%s" % name,
header, outFun)
print(web.linkFile(studyName, "cmp.top.%s" % name, "(download)", isStudy=True, fType="text/plain"))
elif study.comparisons.getType(name)=="Pair":
os.chdir(MEGA.cacheDB + "/studies/"+studyName)
f = open("cmp.pr.%s" % name)
print("<table>")
for l in f:
print("<tr><td>")
print("</td><td>".join(l.rstrip().split("\t")))
print("</td></tr>")
print("</table>")
print(web.linkFile(studyName, "cmp.pr.%s" % name, "(download)", isStudy=True, fType="text/plain"))
print("<br>")
print(web.linkFile(studyName, "cmp.p2.%s" % name, "Windows", isStudy=True, fType="text/plain"))
elif study.comparisons.getType(name)=="Gene List":
os.chdir(MEGA.cacheDB + "/studies/"+studyName)
f = open("cmp.gl.%s" % name)
try:
f = open("%s/sets/%s/%s/basic" % (MEGA.cacheDB, karyo, md5))
print("<table border=1><tr><td><b>total</b></td><td>%s</td></tr><tr>" % (
f.readline(),))
for l in f:
print("<tr><td>")
print("</td><td>".join(l.split("\t")))
print("</td></tr>")
print("</table>")
except IOError:
print("<br><b>Basic info for this population is not available</b>")
print("<h2>Inbreeding</h2>")
print("<h3>Genome IBD</h3>")
print(web.linkFile((karyo, md5), "genome", "genome file",
errorDesc="genome info not available"))
cuts = []
try:
for name in os.listdir("%s/sets/%s/%s" % (MEGA.cacheDB, karyo, md5)):
if name.startswith("ibd.retain"):
cuts.append(name[11:])
except OSError:
print("No info")
print("<h3>Distant individuals</h3>")
for cut in cuts:
print("<br><b>%s</b><br>" % (cut,))
df = "%s/sets/%s/%s/distant.%s" % (MEGA.cacheDB, karyo, md5, cut)
try:
ids = sql.getIds(md5)
karyo = form["k"].value
myStudies = []
for id in ids:
idStr = id[0]
if idStr.find("iHS"):
toks = idStr.split("/")
myStudies.append(toks[1] + "/" + toks[-1])
web.sendPreamble(md5, None, "iHS")
print('<a href="pop.py?md5=%s">Population page</a>' % (md5,))
print("<h1>iHS</h1>")
print(",".join(myStudies))
print("<h2>Bulk Downloads</h2>")
print(web.linkFile((karyo, md5), "uiHS.zip", "Download bulk data (unstandardized)",))
print(web.linkFile((karyo, md5), "iHS.zip", "Download bulk data (standardized)",))
print(web.linkFile((karyo, md5), "iHS.window", "Download bulk data (Window)",))
print("<h2>Mean, standard deviation</h2>")
try:
print(web.linkFile((karyo, md5), "iHSCheck.png", None,
False, True, attrs='width="30%"'))
print(web.linkFile((karyo, md5), "uiHS.png", None, False,
True, attrs='width="30%"'))
except IOError:
print("Not available")
print("<h2>GO Window enrichment</h2>")
sys.path.insert(0, os.path.expanduser(path))
import MEGA
from MEGA import web
form = cgi.FieldStorage()
op, md5, studyName, study = web.getCore(form)
no = int(form["no"].value)
studyPath = "%s/studies/%s/" % (MEGA.cacheDB, studyName)
web.sendPreamble(md5, None, "F statistics - %s - %d" % (studyName, no))
print("<h1>FST - %s - %d</h1>" % (studyName, no))
print(web.linkFile(studyName, "f%d.zip" % no, "Download bulk data", True))
print("<h2>Populations</h2>")
for pop in study.fs.pops[no]:
print("%s<br>" % pop)
print("<h2>Summary</h2>")
f = open(studyPath + "FST-summary-%d" % no)
header = f.readline()
vals = f.readline()
print("<table border=1><tr><td>")
print("</td><td>".join(header.split("\t")))
print("</td></td><tr><td>")
print("</td><td>".join(vals.split("\t")))
print("</td></td></table>")
