perl kylle345_run.pl /path/to/directory/*.txt

#!/usr/bin/perl
# kylle345_run.pl

use strict;
use warnings;
use File::Copy qw(move);

# process each file given at the command line
for my $fname (@ARGV){
    my $fh;
    # open the current file    
    if(not open $fh, '<', $fname){
        # file could not be read; skip
        print STDERR "$fname could not be processed\n";
        next;
    }
    print "Processing file: $fname ...\n";

    # obtain substrings from file name if not skip
    my @names = $fname =~ /\[(.+?)\]\[\w\]/g or next;
    open my $fh_bk, '>', "$fname.bk" or next;
    my $before_last = "AMEL\tX\tY\t\tX\tX\n";

    # read the current file
    while(<$fh>){
         # only at second line substitute the xxx.fsa with parts of filename
         s/\w{3}\.fsa(\s+)\w{3}\.fsa/$names[0]$1$names[1]/ if $. == 2;
         # add a line before last
         if(eof) {
             print $fh_bk "$before_last$_";
             next;
         }
         # write to a copy ending in .bk
         print $fh_bk $_;
    }
    close $fh;
    close $fh_bk;
    # test first and if it does correctly, remove the
    # # from next line to rename backup to original name
    #move "$fname.bk", $fname;
}

awk '
NR==1   {split(FILENAME, T, "[][]")
        }
NR==2   {sub ("...\.fsa", T[2])
         sub ("...\.fsa", T[6])
         EL="AMEL\tX\t" (T[4]=="M"?"Y":"X") "\t\tX\t" (T[8]=="M"?"Y":"X")
        }
NF==1   {print EL
        }

1

' 'UNIQUEID-LABID_[First Name 1][M] - [First Name 2][F].txt'