Open doRemy opened 4 years ago
Hello,
When computing the GSVA with this method I have this error:
UnsupportedOperation Traceback (most recent call last) <ipython-input-32-ae5824630c90> in <module> 3 geneset_df=test, 4 method='ssgsea', ----> 5 verbose=True 6 ) ~/miniconda3/envs/scRNA1/lib/python3.6/site-packages/GSVA/__init__.py in gsva(expression_df, geneset_df, method, kcdf, abs_ranking, min_sz, max_sz, parallel_sz, parallel_type, mx_diff, tau, ssgsea_norm, verbose, tempdir) 99 destination = PIPE 100 if verbose: destination = sys.stderr --> 101 sp = Popen(cmd,stdout=PIPE,stderr=destination) 102 sp.communicate() 103 output = pd.read_csv(os.path.join(tempdir,"pathways.csv"),index_col=0) ~/miniconda3/envs/scRNA1/lib/python3.6/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors) 685 (p2cread, p2cwrite, 686 c2pread, c2pwrite, --> 687 errread, errwrite) = self._get_handles(stdin, stdout, stderr) 688 689 # We wrap OS handles *before* launching the child, otherwise a ~/miniconda3/envs/scRNA1/lib/python3.6/subprocess.py in _get_handles(self, stdin, stdout, stderr) 1219 else: 1220 # Assuming file-like object -> 1221 errwrite = stderr.fileno() 1222 1223 return (p2cread, p2cwrite, UnsupportedOperation: fileno
Do you know what could be done to solve this issue?
Hello,
When computing the GSVA with this method I have this error:
Do you know what could be done to solve this issue?