def run_all():
"""Run a variety of enrichment analysis."""
fout_log = GOEA.get_fout_log()
log = sys.stdout if fout_log is None else open(fout_log, 'w')
goeaobj = init_goea(log) # Initialize once
test_bonferronis(log, goeaobj)
close_log(fout_log, log)
sort_by = lambda nt: [nt.NS, -1 * nt.depth]
fld2fmt = {"fdr_bh": "{:8.2e}"} # Optional user defined formatting for specific fields
goea.wr_tsv(
fout_tsv, results_nt, field_names, keep_if=keep_if, sort_by=sort_by, fld2fmt=fld2fmt, print_names=print_names
)
# 3. Write results to xlsx file
# Use these headers instead of the print_names for the xlsx header
hdrs = ["NS", "Cnt", "fdr_bh", "L", "D", "Term", "Ontology Term Name"]
# TBD Check that header and size of fields printed match
goea.wr_xlsx(
fout_xls,
results_nt,
field_names,
# optional key-word args (ie, kwargs, kws)
keep_if=keep_if,
sort_by=sort_by,
hdrs=hdrs,
fld2fmt=fld2fmt,
print_names=print_names,
)
if fout_log is not None:
log.close()
sys.stdout.write(" WROTE: {}\n".format(fout_log))
if __name__ == "__main__":
test_fdr_bh(GOEA.get_fout_log())
# Copyright (C) 2016, DV Klopfenstein, H Tang. All rights reserved.
# ...
# Print format field names are the same names as in the "field_names" variable.
prtfmt = " ".join(["{NS} {study_cnt:2} {pval_uncor:5.3e}",
"{bonferroni_star:1} {bonferroni:5.3e} L{level:02} D{depth:02} {GO} {name}\n"])
prt_if = lambda nt: nt.bonferroni_sig # T/F: Keep the GOEA GO Term result only if the result is significant.
goea.prt_txt(log, results_nt, field_names, prtfmt, sort_by=sort_by, prt_if=prt_if)
# 2. Write results to tsv file
# Optional user defined formatting for specific fields
fld2fmt = {'bonferroni':'{:8.2e}', 'pval_uncor':'{:8.2e}'}
# Sort by: 1st) BP, MF, CC; 2nd) By GO depth, deepest GO first.
sort_by = lambda nt: [nt.NS, -1*nt.depth]
goea.wr_tsv(fout_tsv, results_nt, field_names,
prt_if=prt_if, sort_by=sort_by, fld2fmt=fld2fmt, print_names=print_names)
# 3. Write results to xlsx file
# Use these headers instead of the print_names for the xlsx header
hdrs = ['NS', 'Cnt', '*', 'bonferroni', 'L', 'D', 'Term', 'Ontology Term Name']
# TBD Check that header and size of fields printed match
goea.wr_xlsx(fout_xls, results_nt, field_names,
# optional key-word args (ie, kwargs, kws)
prt_if=prt_if, sort_by=sort_by, hdrs=hdrs, fld2fmt=fld2fmt, print_names=print_names)
if fout_log is not None:
log.close()
sys.stdout.write(" WROTE: {}\n".format(fout_log))
if __name__ == '__main__':
test_bonferroni(GOEA.get_fout_log())
# Copyright (C) 2016, DV Klopfenstein, H Tang. All rights reserved.
results_nt,
field_names,
keep_if=keep_if,
sort_by=sort_by,
fld2fmt=fld2fmt,
print_names=print_names)
# 3. Write results to xlsx file
# Use these headers instead of the print_names for the xlsx header
hdrs = ['NS', 'Cnt', 'fdr_bh', 'L', 'D', 'Term', 'Ontology Term Name']
# TBD Check that header and size of fields printed match
goea.wr_xlsx(
fout_xls,
results_nt,
field_names,
# optional key-word args (ie, kwargs, kws)
keep_if=keep_if,
sort_by=sort_by,
hdrs=hdrs,
fld2fmt=fld2fmt,
print_names=print_names)
if fout_log is not None:
log.close()
sys.stdout.write(" WROTE: {}\n".format(fout_log))
if __name__ == '__main__':
test_fdr_bh(GOEA.get_fout_log())
# Copyright (C) 2016, DV Klopfenstein, H Tang. All rights reserved.
