how to set file as a variable in bash -

i new in bash scripting set files variables in loop in bash script. have code:

a=home/my_directory/*.fasta b=home/my_directory/*.aln  in {1..14}   # have 14 files in my_directory file extension .fasta clustalo -i $a -o $b  # clustalo command of clustal omega software, -i                        # input file, -o output file done 

i want use fasta files in my_directory , create 14 new aln files. code doesnt work because clustal program doesnt recognize set files. if can thankful.

if know there 14 files, this:

for in {1..14};     clustalo -i home/my_directory/$a.fasta -o home/my_directory/$b.aln done 

if want process of *.fasta files, many there are, do:

for file in home/my_directory/*.fasta;     clustalo -i "$file" -o "${file%.fasta}.aln" done 

to understand this, ${file%.fasta} gives $file .fasta extension stripped off.

if want store file names in variable first, best thing use array variable. adding parentheses around variable assignment, , accessing array values strange syntax "${array[@]}".

files=(home/my_directory/*.fasta)  file in "${files[@]}";     clustalo -i "$file" -o "${file%.fasta}.aln" done