MixMHCpred not creating mixmhcpred_outputs.txt in tmp dir

[zakimolvi]

I'm a big fan of using mhctools as a python wrapper for NetMHC. I am trying to use it now for MixMHCpred, but I am having the following issue:

Running the following code:

predictor = NetMHCpan(alleles=don_alleles)
predictor2 = MixMHCpred(alleles=don_alleles)
preds = predictor.predict_peptides(sample_peptides)
preds2 = predictor2.predict_peptides(sample_peptides)

Outputs:

File "/Users/zaki/PycharmProjects/HLA_ligands_ALSF/3-bindingPreds.py", line 50, in pan_mix_preds
    preds2 = predictor2.predict_peptides(sample_peptides)
  File "/opt/anaconda3/lib/python3.7/site-packages/mhctools/mixmhcpred.py", line 98, in predict_peptides
    results.extend(parse_mixmhcpred_results(output_file_path))
  File "/opt/anaconda3/lib/python3.7/site-packages/mhctools/mixmhcpred.py", line 116, in parse_mixmhcpred_results
    df = pd.read_csv(filename, comment="#", sep="\t")
  File "/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 676, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 448, in _read
    parser = TextFileReader(fp_or_buf, **kwds)
  File "/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 880, in __init__
    self._make_engine(self.engine)
  File "/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1114, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1891, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 374, in pandas._libs.parsers.TextReader.__cinit__
  File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] File 
/var/folders/d7/8tw42scd6pj3fh6j4mhyj6580000gn/T/mhctoolsl4e89xigmixmhcpred/mixmhcpred_outputs.txt does not exist: 
'/var/folders/d7/8tw42scd6pj3fh6j4mhyj6580000gn/T/mhctoolsl4e89xigmixmhcpred/mixmhcpred_outputs.txt'

The tmp dir in the traceback does exist and contains mixmhcpred_inputs.txt, but not mixmhcpred_outputs.txt. So it seems MixMHCpred is failing to write the outputs. What could cause this?

Other info:

• MixMHCpred dir is in project PATH
• MixMHCpred runs successfully from command line
• predictor.predict_peptides (NetMHCpan) works fine (but predictor2.predict_peptides (MixMHCpred) does not)

[timodonnell]

Not sure what's happening here - could you provide a small working example (with peptides etc) so I can try to reproduce? It would also be helpful to know the mixmhcpred version you have installed and confirm that running mixmhcpred manually yourself works.