print("<br>")
print(study.summary)
print("<h2>Map</h2>")
web.addMap(study.pops.pops)
print("<h2>Populations</h2>")
cuts = study.ibd.cuts
print('<table border="1">')
print('<tr><td>Population</td><td>#</td>')
for cut in cuts:
print('<td>', cut, '</td>')
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 "<title>MEGA browser</title>"
print "<h1>MEGA browser</h1>"
print "<h2>Studies</h2>"
print """
<table border="1">
<tr>
<td>Study</td>
<td>Study pops</td>
<td>Out pops</td>
</tr>
"""
for study in MEGA.studies:
ins, outs = MEGA.studies[study]
inURLs = map(lambda x: web.getPopURL(x), ins)
outURLs = map(lambda x: web.getPopURL(x), outs)
print "<tr><td>%s</td><td>%s</td><td>%s</td></tr>" % (
study, ", ".join(inURLs), ", ".join(outURLs))
print "</table>"
print "<h2>Bundles</h2>"
print """
<table border="1">
<tr>
<td>Bundle</td>
<td>Inside</td>
</tr>
"""
for bundle in MEGA.bundles:
pops = MEGA.bundles[bundle]
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>")
print "<title>MEGA browser</title>"
print "<h1>MEGA browser</h1>"
print "<h2>Studies</h2>"
print """
<table border="1">
<tr>
<td>Study</td>
<td>Study pops</td>
<td>Out pops</td>
</tr>
"""
for study in MEGA.studies:
ins, outs = MEGA.studies[study]
inURLs = map(lambda x:web.getPopURL(x), ins)
outURLs = map(lambda x:web.getPopURL(x), outs)
print "<tr><td>%s</td><td>%s</td><td>%s</td></tr>" % (study, ", ".join(inURLs), ", ".join(outURLs))
print "</table>"
print "<h2>Bundles</h2>"
print """
<table border="1">
<tr>
<td>Bundle</td>
<td>Inside</td>
</tr>
"""
for bundle in MEGA.bundles:
from MEGA import web
form = cgi.FieldStorage()
pop = form["p"].value
print '<a href="mega.py">Main page</a>'
print "<title>%s</title>" % (pop,)
print "<h1>%s</h1>" % (pop,)
isBundle = pop in MEGA.bundles
if isBundle:
mid = "bundles"
print "<h2>Bundle</h2>"
for p in MEGA.bundles[pop]:
print web.getPopURL(p) + ", "
else:
mid = "pops"
print "<b>Core pop</b>"
myBundles = []
for bundle in MEGA.bundles:
if pop in MEGA.bundles[bundle]:
myBundles.append(bundle)
if len(myBundles)>0:
print "I am in the following bundles: %s" %(", ".join(web.getPopsURLs(myBundles)))
print """
<table border="1">
<tr>
<td valign="top">