def init_goea(log):
"""Read Ontologies and Annotations once."""
# ---------------------------------------------------------------------
# Run Gene Ontology Analysis (GOEA)
#
# 1. Initialize
obo_dag = GODag("go-basic.obo")
assoc = read_associations("../data/association", no_top=True)
popul_ids = [line.rstrip() for line in open("../data/population")]
# 2. Run enrichment analysis
goeaobj = GOEA(obo_dag, assoc, log)
goeaobj.set_population(popul_ids)
return goeaobj
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)
def test_bonferroni(fout_log=None):
"""Do Gene Ontology Enrichment Analysis w/Bonferroni multipletest. Print results 3 ways."""
# ---------------------------------------------------------------------
# Run Gene Ontology Analysis (GOEA)
#
# 1. Initialize
log = sys.stdout if fout_log is None else open(fout_log, 'w')
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")]
# 2. Run enrichment analysis
goea = GOEA(obo_dag, assoc, log)
goea.set_population(popul_ids)
goea.set_params(alpha=0.05, method='bonferroni')
results_nt = goea.find_enrichment(study_ids)
# ---------------------------------------------------------------------
# Print results 3 ways: to screen, to tsv (tab-separated file), to xlsx (Excel spreadsheet)
fout_tsv = "goea_bonferroni.tsv"
fout_xls = "goea_bonferroni.xlsx"
# print these in tsv and xlsx
print_names = ['NS', 'study_cnt', 'pval_uncor', 'bonferroni_star', 'bonferroni', 'level', 'depth', 'GO', 'name']
field_names = print_names + ['bonferroni_sig'] # collect this. Used in prt_if
# Optional user customizable sort:
# Sort by: 1st) BP, MF, CC; 2nd) corrected pval, with smallest last.
sort_by = lambda nt: [nt.NS, -1*nt.pval_uncor]
# 1. Print results to screen using format in prtfmt. For example:
#
# BP 22 3.073e-03 L06 D07 GO:0006468 protein phosphorylation
# BP 9 1.023e-02 L07 D08 GO:0006511 ubiquitin-dependent protein catabolic process
# BP 2 1.023e-02 L05 D09 GO:0019877 diaminopimelate biosynthetic process
# BP 2 1.223e-02 L04 D08 GO:0006301 postreplication repair
# BP 2 1.223e-02 L05 D09 GO:0030418 nicotianamine biosynthetic process
# BP 2 1.492e-02 L04 D06 GO:0006909 phagocytosis
# BP 2 1.492e-02 L03 D03 GO:0051322 anaphase
# ...
# 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))
# ...
# 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.
def test_fdr_bh(fout_log=None):
"""Do Gene Ontology Enrichment Analysis w/Benjamini-Hochberg multipletest. Print results"""
# ---------------------------------------------------------------------
# Run Gene Ontology Analysis (GOEA)
#
# 1. Initialize
log = sys.stdout if fout_log is None else open(fout_log, "w")
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")]
# 2. Run enrichment analysis
goea = GOEA(obo_dag, assoc, log)
goea.set_population(popul_ids)
goea.set_params(alpha=0.05, method="fdr_bh")
results_nt = goea.find_enrichment(study_ids)
# ---------------------------------------------------------------------
# Print results 3 ways: to screen, to tsv(tab-separated file), to xlsx(Excel spreadsheet)
fout_tsv = "goea_fdr_bh.tsv"
fout_xls = "goea_fdr_bh.xlsx"
field_names = ["NS", "study_cnt", "fdr_bh", "level", "depth", "GO", "name", "fdr_bh_sig"] # collect these
print_names = ["NS", "study_cnt", "fdr_bh", "level", "depth", "GO", "name"] # print these in tsv and xlsx
# Optional user customizable sort:
# Sort by: 1st) BP, MF, CC; 2nd) corrected pval, with smallest first.
sort_by = lambda nt: [nt.NS, nt.fdr_bh]
# 1. Print results to screen using format in prtfmt. For example:
#
# BP 22 3.073e-03 L06 D07 GO:0006468 protein phosphorylation
# BP 9 1.023e-02 L07 D08 GO:0006511 ubiquitin-dependent protein catabolic process
# BP 2 1.023e-02 L05 D09 GO:0019877 diaminopimelate biosynthetic process
# BP 2 1.223e-02 L04 D08 GO:0006301 postreplication repair
# BP 2 1.223e-02 L05 D09 GO:0030418 nicotianamine biosynthetic process
# BP 2 1.492e-02 L04 D06 GO:0006909 phagocytosis
# BP 2 1.492e-02 L03 D03 GO:0051322 anaphase
# ...
# Print format field names are the same names as in the "field_names" variable.
prtfmt = "{NS} {study_cnt:2} {fdr_bh:5.3e} L{level:02} D{depth:02} {GO} {name}\n"
keep_if = lambda nt: nt.fdr_bh_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, keep_if=keep_if)
# 2. Write results to tsv file
# Sort by: 1st) BP, MF, CC; 2nd) By GO depth, deepest GO first.
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))
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.
def test_fdr_bh(fout_log=None):
"""Do Gene Ontology Enrichment Analysis w/Benjamini-Hochberg multipletest. Print results"""
# ---------------------------------------------------------------------
# Run Gene Ontology Analysis (GOEA)
#
# 1. Initialize
log = sys.stdout if fout_log is None else open(fout_log, 'w')
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")]
# 2. Run enrichment analysis
goea = GOEA(obo_dag, assoc, log)
goea.set_population(popul_ids)
goea.set_params(alpha=0.05, method='fdr_bh')
results_nt = goea.find_enrichment(study_ids)
# ---------------------------------------------------------------------
# Print results 3 ways: to screen, to tsv(tab-separated file), to xlsx(Excel spreadsheet)
fout_tsv = "goea_fdr_bh.tsv"
fout_xls = "goea_fdr_bh.xlsx"
field_names = [
'NS', 'study_cnt', 'fdr_bh', 'level', 'depth', 'GO', 'name',
'fdr_bh_sig'
] # collect these
print_names = [
'NS', 'study_cnt', 'fdr_bh', 'level', 'depth', 'GO', 'name'
] # print these in tsv and xlsx
# Optional user customizable sort:
# Sort by: 1st) BP, MF, CC; 2nd) corrected pval, with smallest first.
sort_by = lambda nt: [nt.NS, nt.fdr_bh]
# 1. Print results to screen using format in prtfmt. For example:
#
# BP 22 3.073e-03 L06 D07 GO:0006468 protein phosphorylation
# BP 9 1.023e-02 L07 D08 GO:0006511 ubiquitin-dependent protein catabolic process
# BP 2 1.023e-02 L05 D09 GO:0019877 diaminopimelate biosynthetic process
# BP 2 1.223e-02 L04 D08 GO:0006301 postreplication repair
# BP 2 1.223e-02 L05 D09 GO:0030418 nicotianamine biosynthetic process
# BP 2 1.492e-02 L04 D06 GO:0006909 phagocytosis
# BP 2 1.492e-02 L03 D03 GO:0051322 anaphase
# ...
# Print format field names are the same names as in the "field_names" variable.
prtfmt = "{NS} {study_cnt:2} {fdr_bh:5.3e} L{level:02} D{depth:02} {GO} {name}\n"
keep_if = lambda nt: nt.fdr_bh_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,
keep_if=keep_if)
# 2. Write results to tsv file
# Sort by: 1st) BP, MF, CC; 2nd) By GO depth, deepest GO first.
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))
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.
