def testExport(self, genes, description, retfile, results):
self.maxDiff = None
enrichr = Enrichr(cutoff = 1)
enrichr.addList(genes, description)
enrichr.enrich()
enrichr.export(retfile)
ret = []
with open(retfile) as f:
for line in f:
line = line.strip()
if not line or line.startswith('Term'): continue
ret.append(Enrichr_Term._make(line.split('\t')))
for i, result in enumerate(results):
for field in result._fields:
rval = getattr(result, field)
oval = getattr(ret[i], field)
if isinstance(rval, (int, float)):
oval = float(oval)
self.assertAlmostEqual(rval, oval, places=3)
else:
self.assertEqual(rval, oval)
def testEnrich(self, genes, description, results): self.maxDiff = None enrichr = Enrichr() enrichr.addList(genes, description) ret = enrichr.enrich() for i, result in enumerate(results): for field in result._fields: rval = getattr(result, field) oval = getattr(ret[i], field) if isinstance(rval, (int, float)): self.assertAlmostEqual(rval, oval) else: self.assertEqual(rval, oval)
if cutoff['by'] == 'p':
cutoff['by'] = 'Pval'
if cutoff['by'] == 'q':
cutoff['by'] = 'AdjPval'
reader = TsvReader(infile, **inopts)
genes = [r[genecol] for r in reader]
en = Enrichr(cutoff = cutoff, top = top, Rscript = Rscript)
en.addList(genes, description = path.basename(infile))
para = Parallel(nthread = nthread)
runPathview = lambda r, hsa: shell.Shell().Rscript(r, hsa).run()
for db in dbs:
outfile = path.join(outdir, prefix + '.' + db + '.txt')
en.enrich(db)
en.export(outfile, top = 100)
if plot:
plotfile = path.join(outdir, prefix + '.' + db + '.png')
en.plot(plotfile, res = devpars.res, width = devpars.width, height = devpars.height)
if pathview and 'KEGG' in db:
pathviewRDir = path.join(outdir, prefix + '.' + db + '.pathview')
pathviewRfile = path.join(pathviewRDir, 'pathview.R')
shell.mkdir(pathviewRDir)
with open(pathviewRfile, 'w') as f:
f.write("""
{rimport}('__init__.r')
library(pathview)
args = commandArgs(trailingOnly = TRUE)
setwd({pathviewRDir!r})
inopts = {{args.inopts | R}}
def testPlot(self, genes, description, plotfile): enrichr = Enrichr(cutoff = 1) enrichr.addList(genes, description) enrichr.enrich() enrichr.plot(plotfile) self.assertGreater(path.getsize(plotfile), 0)