use strict;
use warnings;
use 5.010;

use File::Basename;


my $target_file_ext = '.ptseq';
my $target_file_pattern = "*$target_file_ext";

for my $in_name (glob $target_file_pattern) {
    my ($name) = fileparse($in_name, ($target_file_ext) );

    my $out_1_name = "${name}1.txt";
    my $out_2_name = "${name}2.txt";

    open my $OUT_1, '>', $out_1_name
        or die "Couldn't open $out_1_name: $!";

    open my $OUT_2, '>', $out_2_name
        or die "Couldn't open $out_2_name: $!";

    open my $INFILE, '<', $in_name
        or die "Couldn't open $in_name: $!";

    while (my $line = <$INFILE>) {
        chomp $line;

        #Some $line processing here:
        say {$OUT_1} "$line  ($out_1_name)";
        say {$OUT_2} "$line  ($out_2_name)";
    }

    close $INFILE;
    close $OUT_1;
    close $OUT_2;
}