os.chdir(MEGA.cacheDB + "/sets/" + karyo + '/' + md5)
for fName in os.listdir("."):
if fName.startswith("xpEHH-%s" % sPop) and fName.endswith(".top"):
cut = float(fName[7 + len(sPop):-4])
print("<br><b>Cut:</b>", cut * 100, "%</br>")
print(web.linkFile(karyo, md5, fName, "Download", False))
if cut > 0.01:
continue
f = open(fName)
print('<table border="1">')
print("<tr><td>Chr</td><td>Start</td><td>End</td><td>P</td><td>Annotations</td></tr>")
for l in f:
print("<tr><td>")
print("</td><td>".join(l.rstrip().split("\t")))
print("</td></tr>")
print("</table>")
f.close()
os.chdir(cwd)
print("<h2>Data</h2>")
def outFun(toks):
#XXX size is hardcoded
toks[1] = '<a href="/cgi-bin/mega/gtf.py?k=%d&start=%d&end=%d">%s</a>' % (
int(toks[0]), int(toks[1]) - 100000, int(toks[1]) + 100000, toks[1])
return toks
web.table("xpEHH.py", cgi, "xpEHH-" + sPop + ".window",
["CHR", "pos", "#stats", "Mean"], outFun)
f = open(fName)
print('<table border="1">')
print("<tr><td>Chr</td><td>Start</td><td>End</td><td>P</td><td>Annotations</td></tr>")
for l in f:
toks = l.rstrip().split("\t")
#XXX size is hardcoded
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])
print("<tr><td>")
print("</td><td>".join(toks))
print("</td></tr>")
print("</table>")
f.close()
os.chdir(cwd)
print("<h2>Data</h2>")
os.chdir(MEGA.cacheDB + "/sets/%s/%s" % (karyo, md5))
def outFun(toks):
#XXX size is hardcoded
toks[1] = '<a href="%s/gtf.py?k=%d&start=%d&end=%d">%s</a>' % (
MEGA.webRoot,
int(toks[0]), int(toks[1]) - 100000, int(toks[1]) + 100000, toks[1])
return toks
web.table("iHS.py", cgi, "iHS.window", ["CHR", "pos", "#stats", "Cut",
"Mean", "bucket", "P"], outFun)
os.chdir(cwd)
print("<h1>%s - Comparison (%s) - %s</h1>" % (studyName, study.comparisons.getType(name), name))
print("<h2>Used analysis</h2>")
if study.comparisons.getType(name)=="Overlap":
for stat, cut, statCase in study.comparisons.getOvComponents(name):
if stat == "iHS":
print(web.getRefiHS(study, statCase))
os.chdir(MEGA.cacheDB + "/studies/"+studyName)
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[2]), toks[1])
return toks
web.table("comparison.py", cgi, "cmp.ov.%s" % name,
["CHR", "start", "end", "refs", "genes"], outFun)
elif study.comparisons.getType(name)=="Difference":
for stat, cut, statCase in study.comparisons.getOvComponents(name):
if stat == "iHS":
print(web.getRefiHS(study, statCase))
os.chdir(MEGA.cacheDB + "/studies/"+studyName)
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[2]), toks[1])
return toks
web.table("comparison.py", cgi, "cmp.df.%s" % name,
["CHR", "start", "end", "genes"], outFun)
elif study.comparisons.getType(name)=="Top":
popInfos = list(study.comparisons.getTopPopsInfo(name))
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>")
print("<h2>Maximum over a window</h2>")
for i in range(24):
chro = i + 1
print(web.linkFile(studyName, "Fst-%d-%d.png" % (no, chro), "", True, True))
os.chdir(MEGA.cacheDB + "/studies/" + studyName)
def outFun(toks):
#XXX size is hardcoded
toks[1] = '<a href="%s/gtf.py?k=%s&start=%d&end=%d">%s</a>' % (
MEGA.webRoot,
toks[0], int(toks[1]) - 100000, int(toks[1]) + 100000, toks[1])
return toks
web.table("Fstat.py", cgi, "FST-window-%d" % no, ["CHR", "pos", "max FST", "above 0.1"], outFun)