Various small fixes for v1.0.0a5

[emarinier]

• Modified updatedb's wget to write less to stdout.
• Made sure quast uses the specified contig size.
• "continue" -> "break" when considering mash command size
• Changes the directory mash runs from to reduce to length of file paths.

[emarinier]

@ericenns The solution for using shorter relative paths instead of longer absolute paths involves finding the common path of all input files and working from the directory of the common path. There's a bit of extra logic to handle when there's only 1 input file or multiple input files in completely different directories.

[apetkau]

This looks great @emarinier, awesome fixes 😄. I did have some comments I left.

Also, if I wanted to run this to test, would I just use proksee evaluate on some fasta file with many contigs?

[apetkau]

Thanks so much for all the changes. They all look amazing 😄

When I went to test it though, I got an error. Running like proksee evaluate -o out contigs.fasta gives me the following exception:

Traceback (most recent call last):
  File "~/miniconda3/envs/proksee/bin/proksee", line 8, in <module>
    sys.exit(cli())
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/proksee/commands/cmd_evaluate.py", line 62, in cli
    evaluate(contigs, output, mash_database_path, species, min_contig_length)
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/proksee/commands/cmd_evaluate.py", line 93, in evaluate
    mash_database_path, id_mapping_filename, species_name)
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/proksee/utilities.py", line 62, in determine_species
    species_list = species_estimator.estimate_major_species()
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/proksee/species_estimator.py", line 116, in estimate_major_species
    mash_filename = self.run_mash()
  File "~/miniconda3/envs/proksee/lib/python3.7/site-packages/proksee/species_estimator.py", line 211, in run_mash
    stdout=unsorted_output_file, stderr=NULL)
  File "~/miniconda3/envs/proksee/lib/python3.7/subprocess.py", line 488, in run
    with Popen(*popenargs, **kwargs) as process:
  File "~/miniconda3/envs/proksee/lib/python3.7/subprocess.py", line 800, in __init__
    restore_signals, start_new_session)
  File "~/miniconda3/envs/proksee/lib/python3.7/subprocess.py", line 1551, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '': ''

This same command works when using the version of proksee from the develop branch.

[emarinier]

Thanks Aaron. Good catch. It turns out I needed to take the absolute path of any file I try to take the directory name from, because a relative path without a directory (ex: "contigs.fasta") would return an empty string for the dirname and then subprocess would try to run the process from an empty string directory.

[apetkau]

Everything looks good. Thanks so much Eric.

[apetkau]

I made one other comment about parallel mash screen (just writing this here again so it's part of a review).

[emarinier]

I made one other comment about parallel mash screen (just writing this here again so it's part of a review).

Added in d1071ce

[apetkau]

Looks great. Thanks so much 😄. Sorry about all the change requests and delays in reviewing. You've done a great job with this.