def writeTraitPage(filename, title, desc, commonGenes, pfilter_cutoff):
traitpage = htmltools.createPage(title, scripts={'sorttable.js':'javascript'})
htmltools.pageDescription(traitpage, desc)
traitChi = computeTraitStatistics(commonGenes, pfilter_cutoff)
significance_pairs = [ (i, trait, traitChi[trait][5]) for i, trait in enumerate(traitChi.keys()) ]
significance_levels = [ pval for (i, trait, pval) in significance_pairs ]
FDR = computePermutationTest(traitChi, commonGenes, significance_levels, __ITERATIONS)
FDR_map = dict( [ ( trait, FDR[i] ) for (i, trait, pval) in significance_pairs ] )
traitTable = []
for trait in traitChi:
(cnt, oddsratio, kappa, numgenes, fisher_exact, fisher_p, genes) = traitChi[trait]
fdr_value = FDR_map[trait]
translate = trait.replace(" ","_").replace("/", " or ").replace("\\", " or ")
if len(trait) > 38:
trait = trait[:35] + "..."
alink = "<a href=\"traitlists/%s.html\">%s</a>" % (translate, trait)
entry = [alink, cnt, numgenes, "%.7f" % (fisher_exact), "%.7f" %
(fisher_p), "%.1f" % (oddsratio), "%.4f" % (kappa), fdr_value]
traitTable.append(entry)
traitTable = sorted(traitTable, key=lambda item: -item[1])
htmltools.createTable(
traitpage,
traitTable,
["Disease/Trait", "# RE Genes", "# Trait Genes",
"fisher exact", "p-value", "odds ratio", "kappa",
"FDR"],
"traitlisthead",
None,
["traitcol", "recol", "genecol", "fishercol","pcol",
"oddscol", "kappacol","bencol"],
"sortable", None)
htmltools.endPage(traitpage)
htmltools.savePage(traitpage, filename)
def writeGenePage(output_dir, filename, title, desc, total, geneTable):
genepage = htmltools.createPage(title)
htmltools.pageDescription(genepage, desc)
newTable=[]
for row in geneTable:
drugcount = 0
if row[0] in drugDB.__drugDict:
drugcount = len(drugDB.__drugDict[row[0]])
if os.path.exists(os.sep.join([output_dir,"genelists",row[0]+".html"])):
newTable.append(["<a href=\"genelists/%s.html\">%s</a>" % (row[0], geneDB.__original_names[row[0]]), row[1], drugcount])
else:
newTable.append([geneDB.__original_names[row[0]], row[1], drugcount])
htmltools.createTable(genepage, newTable, ["Gene","#Associated Traits", "#Targeted Drugs"], "genelisthead", None, ["genecol","traitcol", "drugcol"],"genetable",None)
htmltools.endPage(genepage)
htmltools.savePage(genepage, filename)
overlap = commonGenes & studyGenes & drugDB.__geneSet
indexpage.div.open(class_="links")
indexpage.p.open()
indexpage.add("Total overlap of drugbank, GWAS, and Rapidly Evolving geneset: ")
indexpage.a(str(len(overlap)), href="all_genes.html")
if os.path.exists(os.sep.join([output_dir, "DAVID", "david_all.xhtml"])):
indexpage.br()
indexpage.a("DAVID Results", href="DAVID/david_all.xhtml")
indexpage.p.close()
indexpage.div.close()
htmltools.endPage(indexpage)
htmltools.savePage(indexpage, os.sep.join([output_dir, "index.html"]))
print ""
if not skip_listings:
print "Creating trait listings..."
computeTraitGeneLists(studyGenes, drugDB.__geneSet, pfilter_cutoff)
computeTraitDrugLists(studyGenes, drugDB.__geneSet, pfilter_cutoff)
createTraitListingsHTML(os.sep.join([output_dir, "traitlists"]))
print "Creating gene listings..."
createGeneListingsHTML(os.sep.join([output_dir,"genelists"]))
print "Creating referenced HTML gene and trait list reports..."
# write trait frequency tables
