def save_enriched_motifs(df, fname: str) -> None:
"""
Save enriched motifs.
Supported file formats are CSV, TSV, GMT, DAT (pickle), JSON or YAML.
:param df:
:param fname:
:return:
"""
extension = PurePath(fname).suffixes
if is_valid_suffix(extension, 'ctx'):
df.to_csv(fname, sep=suffixes_to_separator(extension))
else:
regulons = df2regulons(df)
if '.json' in extension:
name2targets = {
r.name: list(r.gene2weight.keys())
for r in regulons
}
with openfile(fname, 'w') as f:
f.write(json.dumps(name2targets))
elif '.dat' in extension:
with openfile(fname, 'wb') as f:
pickle.dump(regulons, f)
elif '.gmt' in extension:
GeneSignature.to_gmt(fname, regulons)
elif is_valid_suffix(extension, 'ctx_yaml'):
save_to_yaml(regulons, fname)
else:
raise ValueError("Unknown file format \"{}\".".format(fname))
def save_enriched_motifs(df, fname: str) -> None:
"""
Save enriched motifs.
Supported file formats are CSV, TSV, GMT, DAT (pickle), JSON or YAML.
:param df:
:param fname:
:return:
"""
extension = os.path.splitext(fname)[1].lower()
if extension in FILE_EXTENSION2SEPARATOR.keys():
df.to_csv(fname, sep=FILE_EXTENSION2SEPARATOR[extension])
else:
regulons = df2regulons(df)
if extension == '.json':
name2targets = {
r.name: list(r.gene2weight.keys())
for r in regulons
}
with open(fname, 'w') as f:
f.write(json.dumps(name2targets))
elif extension == '.dat':
with open(fname, 'wb') as f:
pickle.dump(regulons, f)
elif extension == '.gmt':
GeneSignature.to_gmt(fname, regulons)
elif extension in {'.yaml', '.yml'}:
save_to_yaml(regulons, fname)
else:
raise ValueError("Unknown file format \"{}\".".format(fname))
modules,
MOTIF_ANNOTATIONS_FNAME,
client_or_address="custom_multiprocessing",
num_workers=nCores)
print("DEFINED regulons")
else:
if calcRegulonsWithIntermediateDf:
df = prune2df(dbs, modules, MOTIF_ANNOTATIONS_FNAME)
print("defined df")
#regulons = df2regulons(df, NOMENCLATURE)
regulons = df2regulons(df)
else:
regulons = prune(dbs, modules, MOTIF_ANNOTATIONS_FNAME)
print("DEFINED regulons, type:")
print(type(regulons))
#save regulons as binary and as text file
save_to_yaml(regulons, REGULONS_BIN_FNAME)
regulons_txt = open(REGULONS_FNAME, "w")
regulons_txt.write(str(regulons))
regulons_txt.close()
print("SAVED regulons")
regulons = load_from_yaml(REGULONS_BIN_FNAME)
print("LOADED regulons, type:")
print(type(regulons))
#print(regulons)