Thanks again for your prompt help. I really appreciate it. The script works perfect. Although I have a small issue. Actually my input file has multiple duplicate entries. Is there any way to get rid of duplicate entries from the file before starting with the actual analysis that this script does? I was thinking if there is a way to compare the fasta headers before getting rid of them to check if there are duplicate entries? It can be a separate script (which can be run before this one) or can be a part of this script.

Again, thank you so much for your help and time.