def test_wr_methods(log=sys.stdout):
"""Demonstrate printing a subset of all available fields using two methods."""
# 1. Gene Ontology Enrichment Analysis
# 1a. Initialize: Load ontologies, associations, and population gene IDs
nature_data = get_goea_results()
goeaobj = nature_data['goeaobj']
goea_results = nature_data['goea_results']
# 2. Write results
# Write parameters:
# The format_string names below are the same names as in the namedtuple field_names.
prtfmt = "{GO} {NS} {level:>2} {depth:>2} {p_fdr_bh:5.2e} {study_count:>5} {name}\n"
wr_params = {
# Format for printing in text format
'prtfmt' : prtfmt,
# Format for p-values in tsv and xlsx format
'fld2fmt' : {'p_fdr_bh' : '{:8.2e}'},
# Print a subset namedtuple fields, don't print all fields in namedtuple.
'prt_flds' : get_fmtflds(prtfmt)
}
# 2a. Use the write functions inside the GOEnrichmentStudy class.
cwddir = os.getcwd()
tsv_obj = os.path.join(cwddir, 'nbt3102_subset_obj.tsv')
tsv_nts = os.path.join(cwddir, 'nbt3102_subset_nt.tsv')
_wr_3fmt_goeaobj(tsv_obj, goea_results, goeaobj, wr_params, log)
# 2b. Use the write functions from the wr_tbl package to print a list of namedtuples.
_wr_3fmt_wrtbl(tsv_nts, goea_results, wr_params, log)
assert filecmp.cmp(tsv_obj, tsv_nts)
def test_wr_methods(log=sys.stdout):
"""Demonstrate printing a subset of all available fields using two methods."""
# 1. Gene Ontology Enrichment Analysis
# 1a. Initialize: Load ontologies, associations, and population gene IDs
nature_data = get_goea_results()
goeaobj = nature_data['goeaobj']
goea_results = nature_data['goea_results']
# 2. Write results
# Write parameters:
# The format_string names below are the same names as in the namedtuple field_names.
prtfmt = "{GO} {NS} {level:>2} {depth:>2} {p_fdr_bh:5.2e} {study_count:>5} {name}\n"
wr_params = {
# Format for printing in text format
'prtfmt': prtfmt,
# Format for p-values in tsv and xlsx format
'fld2fmt': {
'p_fdr_bh': '{:8.2e}'
},
# Print a subset namedtuple fields, don't print all fields in namedtuple.
'prt_flds': get_fmtflds(prtfmt)
}
# 2a. Use the write functions inside the GOEnrichmentStudy class.
cwddir = os.getcwd()
tsv_obj = os.path.join(cwddir, 'nbt3102_subset_obj.tsv')
tsv_nts = os.path.join(cwddir, 'nbt3102_subset_nt.tsv')
_wr_3fmt_goeaobj(tsv_obj, goea_results, goeaobj, wr_params, log)
# 2b. Use the write functions from the wr_tbl package to print a list of namedtuples.
_wr_3fmt_wrtbl(tsv_nts, goea_results, wr_params, log)
assert filecmp.cmp(tsv_obj, tsv_nts)
def test_wr_methods(log=sys.stdout):
"""Demonstrate printing a subset of all available fields using two methods."""
# 1. Gene Ontology Enrichment Analysis
# 1a. Initialize: Load ontologies, associations, and population gene IDs
taxid = 10090 # Mouse study
geneids_pop = GeneID2nt_mus.keys() # Mouse protein-coding genes
goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
# 1b. Run GOEA
geneids_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
keep_if = lambda nt: getattr(nt, "p_fdr_bh") < 0.05 # keep if results are significant
goea_results = goeaobj.run_study(geneids_study, keep_if=keep_if)
# 2. Write results
# Write parameters:
# The format_string names below are the same names as in the namedtuple field_names.
prtfmt = "{GO} {NS} {level:>2} {depth:>2} {p_fdr_bh:5.2e} {study_count:>5} {name}\n"
wr_params = {
# Format for printing in text format
'prtfmt' : prtfmt,
# Format for p-values in tsv and xlsx format
'fld2fmt' : {'p_fdr_bh' : '{:8.2e}'},
# Print a subset namedtuple fields, don't print all fields in namedtuple.
'prt_flds' : get_fmtflds(prtfmt)
}
# 2a. Use the write functions inside the GOEnrichmentStudy class.
_wr_3fmt_goeaobj(goea_results, goeaobj, wr_params, log)
# 2b. Use the write functions straight from the wr_tbl package to print a list of namedtuples.
_wr_3fmt_wrtbl(goea_results, wr_params, log)
assert filecmp.cmp('nbt3102_subset_obj.tsv', 'nbt3102_subset_nt.tsv')
def prt_txt(self, prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
if prtfmt is None:
prtfmt = "{GO} {NS} {p_uncorrected:5.2e} {study_count:>5} {name}\n"
prtfmt = self.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = get_goea_nts_prt(goea_results, prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts
def prt_txt(self, prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
if prtfmt is None:
prtfmt = "{GO} {NS} {p_uncorrected:5.2e} {study_count:>5} {name}\n"
prtfmt = self.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = get_goea_nts_prt(goea_results, prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts
def prt_txt(self, prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
if prtfmt is None:
prtfmt = ("{GO} {NS} {p_uncorrected:5.2e} {ratio_in_study:>6} {ratio_in_pop:>9} "
"{depth:02} {name:40} {study_items}\n")
prtfmt = self.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = get_goea_nts_prt(goea_results, prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts
def prt_txt(prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
objprt = PrtFmt()
if prtfmt is None:
flds = ['GO', 'NS', 'p_uncorrected',
'ratio_in_study', 'ratio_in_pop', 'depth', 'name', 'study_items']
prtfmt = objprt.get_prtfmt_str(flds)
prtfmt = objprt.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts
def prt_txt(self, prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
objprt = PrtFmt()
if prtfmt is None:
flds = ['GO', 'NS', 'p_uncorrected', 'ratio_in_study', 'ratio_in_pop', 'depth', 'name', 'study_items']
prtfmt = objprt.get_prtfmt_str(flds)
#### prtfmt = " ".join([objprt.default_fld2fmt[f] for f in flds])
#### prtfmt = ("{GO} {NS} {p_uncorrected:5.2e} {ratio_in_study:>6} {ratio_in_pop:>9} "
#### "{depth:02} {name:40} {study_items}\n")
prtfmt = objprt.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
return data_nts
def prt_txt(self, prt, results_nt, prtfmt, **kws):
"""Print GOEA results in text format."""
prtfmt = self.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = self._get_nts(results_nt, prt_flds, True, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
def prt_txt(self, prt, results_nt, prtfmt, **kws):
"""Print GOEA results in text format."""
prtfmt = self.adjust_prtfmt(prtfmt)
prt_flds = RPT.get_fmtflds(prtfmt)
data_nts = self._get_nts(results_nt, prt_flds, True, **kws)
RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)