#!/usr/bin/perl

use strict;
use subs ;
use File::Basename;
use Data::Dumper;
my %parameters = getParams();

my @versions = split(/,/,$parameters{versions});
my @species  = split(/,/,$parameters{species});


open (ATX_FILE, $parameters{file});
my $i=0;
my $seq;

while (<ATX_FILE>)
{

  next if ($_ =~ m/(^[^\d])/);
  chomp;
  my @elements = split (/ +/,$_);
  print "1 $species[0] $parameters{file} $versions[0] $elements[1] $elements[2] $elements[3] + ";
  print   "$species[1] $parameters{file} $versions[1] $elements[4] $elements[5] $elements[6] $elements[7]\n";
  $_ = <ATX_FILE>;
  $seq = maskRepetiveSequence($_);  
  print $seq;
  $_ = <ATX_FILE>;
  $seq = maskRepetiveSequence($_);  
  print $seq;
  print "\n";
}

#print $parameters{files}[0] ."\n";

sub maskRepetiveSequence
{
   my $seq = shift;
   $seq =~ tr/atgc/NNNN/;
   return $seq;
}


sub getParams {
    my %opts;
    my $errstr = "";
    my @species;
    my @versions;
    my @files;
    use Getopt::Long;
 
    GetOptions(\%opts, 'species=s','versions=s','file=s');

    @species  = split(/,/,$opts{species});
    @versions = split(/,/,$opts{versions});

    if ( ! -e $opts{file} )
    {
      $errstr .= "ERROR : File doesn't exist.\n";
    }

    if ((@species != 2) || (@versions != 2))
    {
      $errstr .= "ERROR : All parameters don't have equal number of values\n";
    }

    if ($errstr) {
        print <<"END_USAGE";
Usage: convert_axt.pl [options] 

Options:

-file     <filename>                Fasta File to index
-species  <name>,<name>...          Print debug messages to log file (Default: fasta_index.log)
-versions <version>,<version>...    Version of the sequence


END_USAGE
        print "\n$errstr" if ($errstr);
        die("\n");
    }
    return (
        file     => $opts{file} ,
        species  => $opts{species},
        versions => $opts{versions});
}