problems with writing reslults to a file in rna_dna_norm.py

When I ran biobakery in the wmtx_wmgs workflow it crashed when it reached to the task of rna_dna_norm.py You can follow the description of my problem here: (https://forum.biobakery.org/t/wmgx-wmtx-worfklow-rna-dna-norm-py-failure-why-is-metagenome-needed-in-metatranscriptome-analysis/2856/2)

I will copy the error message I got:

Error executing action 0. Original Exception: 
  Traceback (most recent call last):
    File "~/miniconda3/envs/$ENV_NAME/lib/python3.7/site-packages/anadama2/runners.py", line 201, in _run_task_locally
      action_func(task)
    File "~/miniconda3/envs/$ENV_NAME/lib/python3.7/site-packages/anadama2/helpers.py", line 89, in actually_sh
      ret = _sh(s, **kwargs)
    File "~/miniconda3/envs/$ENV_NAME/lib/python3.7/site-packages/anadama2/util/__init__.py", line 320, in sh
      raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
  anadama2.util.ShellException: [Errno 1] Command `rna_dna_norm.py --input-dna $OUTPUT_PATH/whole_metagenome_shotgun/humann/merged/genefamilies.tsv --input-rna $OUTPUT_PATH/whole_metatranscriptome_shotgun/humann/merged/genefamilies.tsv --output $OUTPUT_PATH/humann/rna_dna_norm/genes --reduce-sample-name' failed. 
  Out: b'Reading RNA table\nReading DNA table\nCompute unstratified features\nNormalize DNA\nNormalize RNA\nCompute stratified features\nNormalize DNA\nNormalize RNA\nCompute only classified features\nNormalize DNA\nNormalize RNA\nWriting unstratified table\n'
  Err: b'Traceback (most recent call last):\n  File "~/miniconda3/envs/$ENV_NAME/bin/rna_dna_norm.py", line 272, in <module>\n    main()\n  File "~/miniconda3/envs/$ENV_NAME/bin/rna_dna_norm.py", line 258, in main\n    output_unstrat_file)\n  File "~/miniconda3/envs/$ENV_NAME/bin/rna_dna_norm.py", line 180, in write_file\n    file_handle.write("\\t".join(column_labels)+"\\n")\nTypeError: a bytes-like object is required, not \'str\'\n'

I think one of the problems of why this task has crashed was because you open the results file using 'wb' mode (i.e. in binary format) instead of simply 'w'. I changed the code in rna_dna_norm.py, line 179 from:

with open(file, "wb") as file_handle:

to:

with open(file, "w") as file_handle:

This helped the code to not crash, however, I don't think it's the last of the problems. As I mentioned in the attached link I also had problems when I included a mapping file mapping RNA sample IDs to the DNA ones.

biobakery / biobakery_workflows

problems with writing reslults to a file in rna_dna_norm.py #18