#! /usr/bin/perl -w

use strict;
use Data::Dumper;

my $fasta_file = $ARGV[0];
my $directory = $ARGV[1];
my $qual_file = $ARGV[2];

sub make_file_hash
{
  my ($file) = @_;
  my %file_hash;

  open(FH, "< $file");
  while (my $line = <FH>) {
    chomp($line);
    my @parts = split(/\//,$line);
    my $name = $parts[3];
    if ($name =~ /(^.{3})([0-9]{4})(F|P|R)/) {
        my $key = $2 . "." . lc($3);
        $file_hash{$key} = $name;
    }
    elsif ($name =~ /(^.{2})([0-9]{8})(F|P|R)/) {
        my $key = $2 . "." . lc($3);
        $file_hash{$key} = $name;
    }
    else {
      print $name . " is crap\n";
    }
  }
  return %file_hash;
}

sub rename
{
  my ($file, $hash_ref, $dir) = @_;
  my %hash = %$hash_ref;
  #print Dumper(%hash);
  if ($file =~ /([0-9]{4,8})(.f|r|p)(.*)/) {
    my $key = $1 . $2;
    if (exists $hash{$key}) {
      my $filename = $hash{$key};
      `mv $file $dir/$filename`;
    }
    else {
      print "no key $key\n";
    }
  }
}

my %tmp_hash = &make_file_hash($fasta_file);

open(FH2, "< $qual_file");
while( my $file = <FH2>) {
  chomp($file);
  &rename($file, \%tmp_hash, $directory)
}