def createTraitListingsHTML(traitListDir):
traitSet = set(gwasDB.__studyByTrait.keys())
for trait in traitSet:
if trait not in __traitMetaAnalysis:
continue
traitMetadata = __traitMetaAnalysis[trait]
RE_proteins = traitMetadata['RE']
drug_proteins = traitMetadata['drugbank']
other_proteins = traitMetadata['other']
chi_RE = traitMetadata['RE_chi']
chi_Drugbank = traitMetadata['drugbank_chi']
traitListFilename = os.sep.join([traitListDir, trait.replace(" ","_").replace("/", " or ").replace("\\", " or ") + ".html"])
traitpage = htmltools.createPage("Trait Summary: " + trait, css_file='../genereport.css')
htmltools.pageDescription(traitpage, "Gene list overlap summary for trait: %s" % (trait))
# two of these
htmltools.createContingencyTable(traitpage, "Overlap with rapidly evolving genes:", "RE", "trait", chi_RE[0], chi_RE[1], chi_RE[2],
chi_RE[3], chi_RE[4], chi_RE[5], chi_RE[6], chi_RE[7] )
htmltools.createContingencyTable(traitpage, "Overlap with drugbank genes:",
"Drugbank", "trait", chi_Drugbank[0], chi_Drugbank[1],
chi_Drugbank[2], chi_Drugbank[3], chi_Drugbank[4],
chi_Drugbank[5], chi_Drugbank[6], chi_Drugbank[7])
chi_drugs = traitMetadata['drugchi']
htmltools.createContingencyTable(traitpage, "Drug contingency for targeting disease vs targeting rapidly evolving proteins:",
"Targets Disease Genes", "Targets RE Genes", chi_drugs[0], chi_drugs[1],
chi_drugs[2], chi_drugs[3], chi_drugs[4],
chi_drugs[5], chi_drugs[6], chi_drugs[7])
traitpage.table.open(class_="invisible")
traitpage.tr.open()
traitpage.td.open()
traitpage.div("Gene Lists:", class_="header")
traitpage.div("Trait genes indicated as rapidly evolving: ", class_="description")
createGeneListTable(traitpage, RE_proteins)
traitpage.div("Trait genes associated with Drugbank targets: ", class_="description")
createGeneListTable(traitpage, drug_proteins)
traitpage.div("Other trait genes: ", class_="description")
createGeneListTable(traitpage, other_proteins)
traitpage.td.close()
traitpage.td.open()
traitpage.div("Drug Lists:", class_="header")
druglistlen = len(__traitMetaAnalysis[trait]['RE_drugs'])
traitpage.div("%d drugs targeting associated rapidly evolving proteins" % (druglistlen), class_="description")
traitpage.div.open(class_="druglist")
traitpage.ul.open()
for drug in __traitMetaAnalysis[trait]['RE_drugs']:
link = "http://www.drugbank.ca/drugs/%s" % (drug)
if drug not in drugDB.__drugs:
traitpage.li(oneliner.a(drug, href=link))
else:
traitpage.li(oneliner.a(drugDB.__drugs[drug]['name'], href=link))
traitpage.ul.close()
traitpage.div.close()
druglistlen = len(__traitMetaAnalysis[trait]['other_drugs'])
traitpage.div("%d Drugs targeting other proteins" % (druglistlen), class_="description")
traitpage.div.open(class_="druglist")
traitpage.ul.open()
for drug in __traitMetaAnalysis[trait]['other_drugs']:
link = "http://www.drugbank.ca/drugs/%s" % (drug)
if drug not in drugDB.__drugs:
traitpage.li(oneliner.a(drug, href=link))
else:
traitpage.li(oneliner.a(drugDB.__drugs[drug]['name'], href=link))
traitpage.ul.close()
traitpage.div.close()
traitpage.td.close()
traitpage.tr.close()
traitpage.table.close()
htmltools.savePage(traitpage, traitListFilename)
print "Making index.html..."
# Report data set properties
indexpage = htmltools.createPage("Rapidly Evolving Gene Meta-Analysis Report")
indexpage.div("Summary of loaded information:", class_="header")
indexpage.div("Rapidly Evolving genes loaded: %d".replace(" ", " ") % (len(studyGenes)),class_="console")
indexpage.div("Drugbank drug target proteins loaded: %d".replace(" ", " ") % (len(drugDB.__geneSet)),class_="console")
indexpage.div("GWAS Genes indicated in disease studies: %d".replace(" ", " ") % (len(gwasDB.__geneSet)),class_="console")
# report gwas, RE overlap chi matrix
htmltools.createContingencyTable(indexpage, "GWAS Overlap with Rapidly Evolving Geneset:", "GWAS", "RE", a1, b1, c1, d1,
oddsratio1, kappa1, fisher_exact1, fisherp1)
indexpage.div.open(class_="links")
indexpage.a("Trait Report", href="gwas_traits.html")
indexpage.a("Gene Listing", href="gwas_genes.html")
if os.path.exists(os.sep.join([output_dir, "DAVID", "david_gwas_common.xhtml"])):
indexpage.br()
indexpage.a("DAVID Results", href="DAVID/david_gwas_common.xhtml")
indexpage.div.close()
# report drugbank, RE overlap chi matrix
indexpage.div.open(class_="reportsquare")
