def doSNPList(comparisons, comparison):
stat, cut = comparisons.getSLStat(comparison)
popInfos = list(comparisons.getSLPopsInfo(comparison))
SNPLists = MEGA.getSNPLists()
SNPListNames = list(SNPLists.keys())
for name in SNPListNames:
w = open("cmp.sl.%s.%s" % (name, comparison), "w")
w.write("\t\t\t")
popInfos = list(comparisons.getGLPopsInfo(comparison))
for popInfo in popInfos:
w.write("\t%s" % (popInfo,))
w.write("\n")
SNPs = SNPLists[name]
winContentSNP = {}
winContentGenes = {}
winSpot = {}
for i in range(len(SNPs)):
winContentSNP.setdefault((SNPs[i][1], SNPs[i][2] -
SNPs[i][2] % 200000),
[]).append(SNPs[i])
for popInfo in popInfos:
popName = popInfo[0]
if len(popInfo) > 1:
suppPop = popInfo[1]
else:
suppPop = None
md5, fName = comparisons.getGLFileName(popName, stat, cut, suppPop)
f = open("%s/sets/%s/%s/%s" % (MEGA.cacheDB, args.karyo,
md5, fName))
for l in f:
toks = l.rstrip().split("\t")
chro = int(toks[0])
pos = int(toks[1])
if (chro, pos) not in list(winContentSNP.keys()):
continue
if len(toks) > 4:
windMarkers = toks[4].split(" ")
else:
windMarkers = []
winContentGenes[(chro, pos)] = windMarkers
winSpot.setdefault((chro, pos), []).append(popName)
for chro, pos in winSpot:
w.write("%d\t%d\t%s\t%s" % (
chro, pos,
" ".join([x[0] + " " + str(x[2])
for x in winContentSNP[chro, pos]]),
" ".join(winContentGenes[chro, pos])))
for popInfo in popInfos:
popName = popInfo[0]
w.write("\t")
if popName in winSpot[(chro, pos)]:
w.write("X")
w.write("\n")
w.close()
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)
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.gl.%s" % name, "(download)", isStudy=True, fType="text/plain"))
elif study.comparisons.getType(name)=="SNP List":
os.chdir(MEGA.cacheDB + "/studies/"+studyName)
snpLists = MEGA.getSNPLists()
for lst in snpLists:
f = open("cmp.sl.%s.%s" % (lst,name))
print(lst)
print("<table border=1>")
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.sl.%s.%s" % (lst,name), "(download)", isStudy=True, fType="text/plain"))
