def test_goea():
"""Test GOEA with method, fdr."""
obo_dag = GODag("go-basic.obo")
assoc = read_associations("../data/association", no_top=True)
popul_ids = [line.rstrip() for line in open("../data/population")]
study_ids = [line.rstrip() for line in open("../data/study")]
goeaobj = GOEnrichmentStudy(popul_ids, assoc, obo_dag, methods=['fdr'])
goea_results = goeaobj.run_study(study_ids)
goeaobj.print_summary(goea_results)
"background population. Please check.\n".format(overlap))
assoc = read_associations(assoc_fn)
methods = args.method.split(",")
obo_dag = GODag(obo_file=args.obo)
propagate_counts = not args.no_propagate_counts
g = GOEnrichmentStudy(pop, assoc, obo_dag,
propagate_counts=propagate_counts,
alpha=args.alpha,
pvalcalc=args.pvalcalc,
methods=methods)
results = g.run_study(study)
if args.outfile is None:
g.print_summary(results, min_ratio=min_ratio, indent=args.indent, pval=args.pval)
else:
# Users can print to both tab-separated file and xlsx file in one run.
outfiles = args.outfile.split(",")
prt_if = None # Print all values
if args.pval is not None:
# Only print out when uncorrected p-value < this value.
prt_if = lambda nt: nt.p_uncorrected < args.pval
for outfile in outfiles:
if outfile.endswith(".xlsx"):
g.wr_xlsx(outfile, results, prt_if=prt_if)
else:
g.wr_tsv(outfile, results, prt_if=prt_if)
# Copyright (C) 2010-2016, H Tang et al., All rights reserved.
assoc = read_associations(assoc_fn)
methods = args.method.split(",")
if args.fdr:
methods.append("fdr")
obo_dag = GODag(obo_file=args.obo)
propagate_counts = not args.no_propagate_counts
g = GOEnrichmentStudy(pop, assoc, obo_dag,
propagate_counts=propagate_counts,
alpha=args.alpha,
methods=methods)
results = g.run_study(study)
if args.outfile is None:
g.print_summary(results, min_ratio=min_ratio, indent=args.indent, pval=args.pval)
else:
# Users can print to both tab-separated file and xlsx file in one run.
outfiles = args.outfile.split(",")
prt_if = None # Print all values
if args.pval is not None:
# Only print out when uncorrected p-value < this value.
prt_if = lambda nt: nt.p_uncorrected < args.pval
for outfile in outfiles:
if outfile.endswith(".xlsx"):
g.wr_xlsx(outfile, results, prt_if=prt_if)
else:
g.wr_tsv(outfile, results, prt_if=prt_if)
# Copyright (C) 2010-2016, H Tang et al., All rights reserved.
