jason-weirather / GSVA

A command-line interface and python module for R's GSVA bioconductor package
Apache License 2.0
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Error UnsupportedOperation: fileno #4

Open doRemy opened 4 years ago

doRemy commented 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?