Short bash for removing duplicates of sequences from a fasta file (keeping one copy of each unique sequence)

remove_duplicate_sequence.shx

#!bin/bash
# remove_duplicate_sequence.shx is a short bash to remove multiple copies of sequences from an input fasta file and saves the result in an output fasta file.
# the bash script was based on Pierre Lindenbaum's script: https://www.biostars.org/p/3003/#3008
# input:
# -f | --file  : fasta file
# -o | --output : output file after removing all the sequences
#
while [ "$1" != "" ]; do
        case $1 in
                -f | --file ) shift
                        fileName=$1
                        ;;
                -o | --output ) shift
                        outputFile=$1
                        ;;
                * ) exit 1
        esac
        shift
done
# The following pipline is composed of the following actions:
# in every row that starts with '>' put '@' at the end of the row
# replace '>' with '#'
# remove the break lines, replace '#' with a breakline, replace '@' with a tab
# sort the file according to the second column (sequences). the -u option keeps only one copy of each unique string.
# add '>' at the begining of each line
# sustitute tab (\t)  with a breakline (\n)
# remove the first line (it's a blank line) and save the result into $output

        sed '/^>/s/$/@/' < $fileName |
        sed 's/^>/#/' |\
        tr -d '\n' | tr "#" "\n" | tr "@" "\t" |\
        sort -u -f -k 2,2  |\
        sed -e 's/^/>/' |\
        tr '\t' '\n/' |\
        tail -n +2 > $outputFile

# End of remove_duplicate_sequence.shx

Hi, Thanks for the script. I have a quick question. Where I could specify the filename in while loop? Thank you