def wr_py_goea_results(self, fout_py, goea_results, **kws):
"""Save GOEA results into Python package containing list of namedtuples."""
var_name = kws.get("var_name", "goea_results")
docstring = kws.get("docstring", "")
sortby = kws.get("sortby", None)
if goea_results:
from goatools.nt_utils import wr_py_nts
nts_goea = goea_results
# If list has GOEnrichmentRecords or verbose namedtuples, exclude some fields.
if hasattr(goea_results[0], "_fldsdefprt") or hasattr(
goea_results[0], 'goterm'):
# Exclude some attributes from the namedtuple when saving results
# to a Python file because the information is redundant or verbose.
nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
docstring = "\n".join(
[docstring, "# {VER}\n\n".format(VER=self.obo_dag.version)])
assert hasattr(nts_goea[0], '_fields')
if sortby is None:
sortby = lambda nt: [
getattr(nt, 'namespace'),
getattr(nt, 'enrichment'),
getattr(nt, 'p_uncorrected'),
getattr(nt, 'depth'),
getattr(nt, 'GO')
]
nts_goea = sorted(nts_goea, key=sortby)
wr_py_nts(fout_py, nts_goea, docstring, var_name)
def wr_py_goea_results(self, fout_py, goea_results, **kws):
"""Save GOEA results into Python package containing list of namedtuples."""
var_name = kws.get("var_name", "goea_results")
docstring = kws.get("docstring", "")
sortby = kws.get("sortby", None)
if goea_results:
from goatools.nt_utils import wr_py_nts
nts_goea = goea_results
# If list has GOEnrichmentRecords or verbose namedtuples, exclude some fields.
if hasattr(goea_results[0], "_fldsdefprt") or hasattr(goea_results[0], 'goterm'):
# Exclude some attributes from the namedtuple when saving results
# to a Python file because the information is redundant or verbose.
nts_goea = get_goea_nts_prt(goea_results)
docstring = "\n".join([docstring, "# {OBO_VER}\n\n".format(OBO_VER=self.obo_dag.version)])
assert hasattr(nts_goea[0], '_fields')
if sortby is None:
sortby = lambda nt: getattr(nt, 'p_uncorrected')
nts_goea = sorted(nts_goea, key=sortby)
wr_py_nts(fout_py, nts_goea, docstring, var_name)
def wr_py_goea_results(self, fout_py, goea_results, **kws):
"""Save GOEA results into Python package containing list of namedtuples."""
var_name = "goea_results" if "var_name" not in kws else kws["var_name"]
docstring = "" if "docstring" not in kws else kws["docstring"]
if goea_results:
from goatools.nt_utils import wr_py_nts
nts_goea = goea_results
# If list has GOEnrichmentRecords or verbose namedtuples, exclude some fields.
if hasattr(goea_results[0], "_fldsdefprt") or hasattr(
goea_results[0], 'goterm'):
# Exclude some attributes from the namedtuple when saving results
# to a Python file because the information is redundant or verbose.
nts_goea = get_goea_nts_prt(goea_results)
docstring = "\n".join([
docstring,
"# {OBO_VER}\n\n".format(OBO_VER=self.obo_dag.version)
])
assert hasattr(nts_goea[0], '_fields')
nts_goea = sorted(nts_goea,
key=lambda nt: getattr(nt, 'p_uncorrected'))
wr_py_nts(fout_py, nts_goea, docstring, var_name)
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)
