Replace test with "${filename%.faa}" to get the name of the file with .faa removed. You should also quote "${filename}" to avoid problems in case of filenames with spaces.
#!/bin/sh for filename in *.faa ; do python predict_genome.py \ --fasta_path /Users/mvalvano/DeepSecE/myruns/"${filename}" \ --model_location /Users/mvalvano/DeepSecE/model/checkpoint.pt \ --data_dir data \ --out_dir myruns/"${filename%.faa}" \ --save_attn --no_cuda done exit 0 With input files
bar.faa foo.faa the script will run
python predict_genome.py --fasta_path /Users/mvalvano/DeepSecE/myruns/bar.faa --model_location /Users/mvalvano/DeepSecE/model/checkpoint.pt --data_dir data --out_dir myruns/bar --save_attn --no_cuda python predict_genome.py --fasta_path /Users/mvalvano/DeepSecE/myruns/foo.faa --model_location /Users/mvalvano/DeepSecE/model/checkpoint.pt --data_dir data --out_dir myruns/foo --save_attn --no_cuda Possible problems with this script:
Since you specify --fasta_path /Users/mvalvano/DeepSecE/myruns/"${filename}", your script will only work without error if the current directory is /Users/mvalvano/DeepSecE/myruns/ or if this directory contains at least the same set of *.faa files as the current directory. (*.faa will expand to the file names in the current directory.)
When /Users/mvalvano/DeepSecE/myruns/ is the current directory, the argument --out_dir myruns/foo might expect or create a directory /Users/mvalvano/DeepSecE/myruns/myruns/foo with double myruns.
