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_wrpy():
"""Test writing GOATOOLS GOEA results to a Python module as a list of nts."""
# Run GOATOOLS Gene Ontology Enrichment Analysis
nature_data = get_goea_results()
# Convert GOATOOLS GOEA results into a list of namedtuples
goea_results = [nt for nt in nature_data['goea_results'] if nt.p_fdr_bh < 0.05]
nts_goea = get_goea_nts_prt(goea_results)
_run(nts_goea, next(iter(nts_goea))._fields)
def test_wrpy():
"""Test writing GOATOOLS GOEA results to a Python module as a list of nts."""
# Run GOATOOLS Gene Ontology Enrichment Analysis
nature_data = get_goea_results()
# Convert GOATOOLS GOEA results into a list of namedtuples
goea_results = [
nt for nt in nature_data['goea_results'] if nt.p_fdr_bh < 0.05
]
nts_goea = get_goea_nts_prt(goea_results)
_run(nts_goea, next(iter(nts_goea))._fields)
def test_gosubdag():
"""Test all ways to make a GoSubDag."""
# Get data to use for test
res = get_goea_results() #
godag = res['obo_dag']
goea_results = res['goea_results']
goids = [r.GO for r in goea_results]
num_goids = len(goids)
# Test Arg: goea_results (list of GOEnrichmentRecord objects)
go_sources = [rec.GO for rec in goea_results]
go2obj = {rec.GO: rec.goterm for rec in goea_results}
gosubdag = GoSubDag(go_sources, go2obj)
assert len(gosubdag.go_sources) == len(goea_results)
# Test Arg: godag (GODag object)
gosubdag = GoSubDag(None, godag)
assert len(gosubdag.go_sources) > 40000
# Test Arg: goids, godag
gosubdag = GoSubDag(goids, godag)
assert len(gosubdag.go_sources) == num_goids
def test_wrpy():
"""Test writing GOATOOLS GOEA results to a Python module as a list of nts."""
# 1. Run GOATOOLS Gene Ontology Enrichment Analysis
nature_data = get_goea_results()
# 2. Convert GOATOOLS GOEA results into a list of namedtuples
goea_results = nature_data['goea_results']
nts_goea = get_goea_nts_prt(goea_results)
# 3. Save GOATOOLS GOEA into a Python module
# 3a. Python module name
module_name = "nbt3102_goea"
fout_py = get_fout_py(module_name)
# 3b. Save GOATOOLS GOEA into a Python module
wr_py_nts(fout_py, nts_goea, varname="nts")
# 4. Check results
nts_py = importlib.import_module(module_name).nts
assert len(nts_goea) == len(nts_py)
# Alternatively, save module through goea object
module_name = "nbt3102_goea_alt"
fout_py = get_fout_py(module_name)
nature_data['goeaobj'].wr_py_goea_results(fout_py, goea_results)
nts_py = importlib.import_module(module_name).goea_results
assert len(nts_goea) == len(nts_py)
def test_wrpy():
"""Test writing GOATOOLS GOEA results to a Python module as a list of nts."""
# 1. Run GOATOOLS Gene Ontology Enrichment Analysis
nature_data = get_goea_results()
# 2. Convert GOATOOLS GOEA results into a list of namedtuples
goea_results = nature_data['goea_results']
nts_goea = get_goea_nts_prt(goea_results)
# 3. Save GOATOOLS GOEA into a Python module
# 3a. Python module name
module_name = "nbt3102_goea"
fout_py = get_fout_py(module_name)
# 3b. Save GOATOOLS GOEA into a Python module
wr_py_nts(fout_py, nts_goea, varname="nts")
# 4. Check results
nts_py = importlib.import_module(module_name).nts
assert len(nts_goea) == len(nts_py)
# Alternatively, save module through goea object
module_name = "nbt3102_goea_alt"
fout_py = get_fout_py(module_name)
nature_data['goeaobj'].wr_py_goea_results(fout_py, goea_results)
nts_py = importlib.import_module(module_name).goea_results
assert len(nts_goea) == len(nts_py)
