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)
def createGeneListingsHTML(geneListDir):
pbar = ProgressBar()
pbar.setMaximum(len(gwasDB.__geneSet))
pbar.updateProgress(0)
i=0
for gene in gwasDB.__geneSet:
if i % 10 == 0:
pbar.updateProgress(i)
i+=1
genePage = htmltools.createPage("Gene Summary: " +
geneDB.__original_names[gene], css_file='../genereport.css',
scripts = {'../sorttable.js':'javascript'})
# Create the disease trait tables
traits = []
for trait in gwasDB.__traitDict[gene]:
traits.append(trait)
traits = sorted(traits, key=lambda trait: -__traitMetaAnalysis[trait]['RE_chi'][0])
traitTable = []
for trait in traits:
cnt = len(__traitMetaAnalysis[trait]['RE'])
oddsratio = __traitMetaAnalysis[trait]['RE_chi'][4]
kappa = __traitMetaAnalysis[trait]['RE_chi'][5]
fisher_exact = __traitMetaAnalysis[trait]['RE_chi'][6]
fisherp = __traitMetaAnalysis[trait]['RE_chi'][7]
numgenes = __traitMetaAnalysis[trait]['geneset_size']
translate = trait.replace(" ","_").replace("/", " or ").replace("\\", " or ")
if len(trait) > 38:
trait = trait[:35] + "..."
traitTable.append(["<a href=\"../traitlists/%s.html\">%s</a>" %
(translate,trait), cnt, numgenes, "%.7f" % (fisher_exact),
"%.7f" % (fisherp), "%.1f" % (oddsratio), "%.4f" % (kappa), ])
genePage.div("Gene %s, total traits: %d" % (geneDB.__original_names[gene],len(traitTable)), class_="header")
htmltools.createTable(genePage, traitTable, ["Disease/Trait", "#RE Genes",
"#Trait Genes", "fisher exact", "P-value",
"oddsratio", "kappa"], "traitlisthead", None,
["traitcol","recol",
"genecol","fishercol","pcol",
"oddscol","kappacol"], "sortable", None)
# Create drug bank links
if gene not in drugDB.__drugDict:
genePage.div("No drugs target gene %s" % (geneDB.__original_names[gene]), class_="header")
else:
drugbank_size = len(drugDB.__drugDict[gene])
genePage.div("%d drugs targeting gene %s" % (drugbank_size, geneDB.__original_names[gene]), class_="header")
genePage.div.open(class_="druglist")
genePage.ul.open()
for drug in drugDB.__drugDict[gene]:
link = "http://www.drugbank.ca/drugs/%s" % (drug)
if drug not in drugDB.__drugs:
genePage.li(oneliner.a(drug, href=link))
else:
genePage.li(oneliner.a(drugDB.__drugs[drug]['name'], href=link))
genePage.ul.close()
genePage.div.close()
htmltools.savePage(genePage, os.sep.join([geneListDir, gene + ".html"]))
pbar.finalize()
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)
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