def createGeneListTable(page, genes, verify=None):
output_list = []
total = 0
for pair in genes:
geneSym, l = pair
total += l
if geneSym in drugDB.__drugDict:
drugs = len(drugDB.__drugDict[geneSym])
else:
drugs = 0
if verify==None or geneSym in verify:
output_list.append(["<a href=\"../genelists/%s.html\" > %s </a>" % (geneSym, geneDB.__original_names[geneSym]), l, drugs])
else:
output_list.append([geneDB.__original_names[geneSym], l, drugs])
output_list = sorted(output_list, key=lambda item: -item[1])
htmltools.createTable(page, output_list, ["Gene", "#Associated Traits", "#Targeted Drugs"], "genelisthead", None, ["genecol","traitcol", "drugcol"],"genetable",None)
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()
