CODEWITHSUNDEEP
pythonargparse
Ryohei
Ryohei

Reputation: 29

How to solve an error with "unrecognized argument"?

I have written (with a lot of aid from my friend) a python script that allows me to:

  1. Search multiple directories for files with the identical names
  2. Append the absolute path to the name of the file
  3. Add all the files to one directory

This was done to avoid files getting overwritten when using the cp command.

Recently I have tried using the script but I now get an error like this:

python ~/gatherfiles.py —outdir protein_files —trgfile  ./*/protein.faa`

error:

gatherfiles.py: error: unrecognized arguments: ./GCF_000374525.1_ASM37452v1_genomic.fna_dfast/protein.faa ./GCF_000463742_ASM94337v1_genomic.fna_dfast/protein.faa ./GCF_...etc.

Does anybody know how to overcome this issue?

Here is the actual script:

_all__ = ['gatherfiles']
import os
import glob
import shutil
import argparse

def gatherfiles(outdirpath, trgfilename):
  """
  Args:
  - outdirpath (str): A path to output directory.
  - trgfilename (str): A name of target file. Escape sequence is available (eg. '*.txt').
  """

  # make output dir
  os.makedirs(outdirpath, exist_ok=True)

  # search target file
  paths = glob.glob(trgfilename, recursive=True)

  for path in paths:
    dname = os.path.dirname(path).split('/')[-1]
    fname = path.split('/')[-1]
    shutil.copyfile(path, os.path.join(outdirpath,dname+'_'+fname))

if __name__ == '__main__':
  parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

  parser.add_argument('--outdir', type=str, required=True, help='path to output directory.')
  parser.add_argument('--trgfile', type=str, required=True, help='name of target file.')
  opt = parser.parse_args()

  gatherfiles(opt.outdir, opt.trgfile)

I expect the newly-named files to be stored in an output file without being overwritten by each other.

Upvotes: 1

Views: 13095

Answers (2)

Useless
Useless

Reputation: 67733

You're running this from the shell, which does its own glob expansion. If you want to pass the argument 

./*/protein.faa

to your program un-expanded, you need to escape it to protect it from the shell, eg.

'./*/protein.faa'

Alternatively, as Taek said, you can change your function and arg parser to accept a pre-expanded list of target paths.

Upvotes: 1

Taek
Taek

Reputation: 1024

Your parser's argument --trgfile takes one string. But you call your script with a wildcard: —trgfile ./*/protein.faa.

This wildcard is then evaluated to multiple strings hence the unrecognized argument error.

Either change the trgfile to accept multiple values (add nargs='+') or call your script with a single trgfile.

Upvotes: 1

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