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")