#!/usr/bin/perl
use strict;
use warnings;
use POSA::Read;

my $seq_vect_file = '/your_path_to/vector_primer';
my $screen_seq_file = '/your_path_to/some_seq.seq';

my $file_of_filenames = shift;

foreach my $abi_file ( <FOFN> ) {
  chomp $abi_file;

  my $read = POSA::Read->importFromAbi(name => $abi_file, file => $abi_file );
  $read->qclip(w => 30);
  $read->seqvectclip(v => $seq_vect_file );
  $read->screenseq(S => $screen_seq_file );

  print $read->asPrimer3, "\n";
}