while(my $key = each %seqInfo) { my $nameWithoutFastaSign = $key; $nameWithoutFastaSign =~ tr/>//d; my $currentDir = getcwd; chdir "$currentDir/$nameWithoutFastaSign"; my $changedDir = getcwd; print "changed directory is: $changedDir\n"; while($fastaFile = glob("*.fasta")) { print "$fastaFile\n"; } chdir "$currentDir"; } #### changed directory is: /home/ammarah/Documents/code/1elwA .fasta changed directory is: /home/ammarah/Documents/code/1ghwA .fasta changed directory is: /home/ammarah/Documents/code/1flwA .fasta