For loop in bash to input a new file in directory

Question

For context: I am running Prokka (as a novice bioinformatician with no Prokka and little Bash experience) and I have multiple FASTA files.

I have been told I need to produce a Bash loop that will allow me to input the FASTA files 1 by 1.

For example: my directory with all the FASTA (.fna) files is called StaphFNA, it has 1000 FASTA files in there. They are all named with ID numbers - but they do not increment as normal (so they aren't numbered 1, 2, 3 etc) there are random jumps e.g., one first be 34872 and the next one is 8933.

I need the first FASTA file within StaphFNA to be inputted, processed in Prokka, then outputted to a file called 'StaphProkka', then the 2nd FASTA file to go through the same process - being outputted into 'StaphProkka' again. On and on until all 1000 are complete.

As you can imagine, its a bit laborious having to do this 1000 times, so I wish to make a loop, but I am new to bash and I am struggling.

My Prokka argument (which I believe to be correct):

prokka /Users/me/Documents/StaphFNA --outdir StaphProkka --prefix staph_aur --kingdom bacteria --locusting staphylococcus

My For loop (which I know is wrong):

i = 0
for i in StaphFNA/.fna*; do
    prokka /Users/me/Documents/StaphFNA/$i --outdir StaphProkka --prefix staph_aur --kingdom bacteria --locusting staphylococcus
i = i + 1
done

Answer 1

If you don't need to specify an output file and prokka produces differently named files based on its input, all you need is:

for file in /Users/me/Documents/StaphFNA/*.fna; do
    prokka "$file" \ 
        --outdir StaphProkka \
        --prefix staph_aur \
        --kingdom bacteria \
        --locusting staphylococcus 
done

The for variable in dir/* pattern will iterate over every file or directory in dir/ and save its pathname as $variable, so you don't need a counter or anything else. If you did need to use a counter, for example to deal with file1.fa, file2.fa etc, and didn't want to also deal with otherfile.fa, you would so something like this (note the lack of spaces around the =, that's iportant):

for ((i=0; i<=10; i++)); do
    someCommand "file${i}.fa"
done

Or, if you need to explicitly increment the counter (which is rare), you could do:

i=0
while [ "$i" -le 10 ]; do
    echo someCommand "file${i}.fa"
    (( i++ ))
done