#!/usr/bin/perl

use strict;
require XML::Simple;
use Data::Dumper;
use subs;

my %args = getParams();
my $xml_file = new XML::Simple();
my $probes = $xml_file->XMLin($args{inputfile}, keyattr => {});
my @index;

for (my $i=0; $i<@{$probes->{probe}}; $i++)
{
  push @index, [$i, $probes->{probe}->[$i]->{species}->[0]->{probe_start}]; 
}

@index = sort { $a->[1]  <=> $b->[1] } @index;
open (OUTFILE,">".$args{outputfile});

for (my $i=0; $i<@index; $i++)
{
  #print $probes->{probe}->[$index[$i][0]]->{species}->[0]]->{probe_start} . "\n";
  printf OUTFILE  "   <probe>\n";  
  printf OUTFILE  "      <time>%s</time>\n", $probes->{probe}->[$index[$i][0]]->{time};
  printf OUTFILE  "      <date>%s</date>\n",$probes->{probe}->[$index[$i][0]]->{date};
  printf OUTFILE  "      <name></name>\n";
  printf OUTFILE  "      <length>%d</length>\n",$probes->{probe}->[$index[$i][0]]->{length};
  printf OUTFILE  "      <alignment_identity>%d</alignment_identity>\n",$probes->{probe}->[$index[$i][0]]->{alignment_identity};
  printf OUTFILE  "      <probe_identity>%d</probe_identity>\n",$probes->{probe}->[$index[$i][0]]->{probe_identity};
  printf OUTFILE  "      <transversions>%d</transversions>\n", $probes->{probe}->[$index[$i][0]]->{transversions};
  printf OUTFILE  "      <transitions>%d</transitions>\n",$probes->{probe}->[$index[$i][0]]->{transitions};
  printf OUTFILE  "      <gaps>%d</gaps>\n", $probes->{probe}->[$index[$i][0]]->{species}->[0]->{gaps};
  printf OUTFILE  "      <probe_alignment>%s</probe_alignment>\n", $probes->{probe}->[$index[$i][0]]->{probe_alignment};
  printf OUTFILE  "      <species id='1'>\n";
  printf OUTFILE  "         <name>%s</name>\n",$probes->{probe}->[$index[$i][0]]->{species}->[0]->{name};
  printf OUTFILE  "         <file>%s</file>\n",$probes->{probe}->[$index[$i][0]]->{species}->[0]->{file};
  printf OUTFILE  "         <version>%s</version>\n",$probes->{probe}->[$index[$i][0]]->{species}->[0]->{version};
  printf OUTFILE  "         <alignment_start>%d</alignment_start>\n",$probes->{probe}->[$index[$i][0]]->{species}->[0]->{alignment_start};
  printf OUTFILE  "         <alignment_end>%d</alignment_end>\n",$probes->{probe}->[$index[$i][0]]->{species}->[0]->{alignment_end};
  printf OUTFILE  "         <chromosome>%s</chromosome>\n", $probes->{probe}->[$index[$i][0]]->{species}->[0]->{chromosome};
  printf OUTFILE  "         <alignment_strand>%s</alignment_strand>\n",$probes->{probe}->[$index[$i][0]]->{species}->[0]->{alignment_strand};
  printf OUTFILE  "         <probe_start>%d</probe_start>\n", $probes->{probe}->[$index[$i][0]]->{species}->[0]->{probe_start};
  printf OUTFILE  "         <probe_end>%d</probe_end>\n", $probes->{probe}->[$index[$i][0]]->{species}->[0]->{probe_end};
  printf OUTFILE  "         <sequence>%s</sequence>\n", $probes->{probe}->[$index[$i][0]]->{species}->[0]->{sequence};
  printf OUTFILE  "      </species>\n";
  printf OUTFILE  "      <species id='2'>\n";
  printf OUTFILE  "         <name>%s</name>\n",$probes->{probe}->[$index[$i][0]]->{species}->[1]->{name};
  printf OUTFILE  "         <file>%s</file>\n",$probes->{probe}->[$index[$i][0]]->{species}->[1]->{file};
  printf OUTFILE  "         <version>%s</version>\n",$probes->{probe}->[$index[$i][0]]->{species}->[1]->{version};
  printf OUTFILE  "         <alignment_start>%d</alignment_start>\n",$probes->{probe}->[$index[$i][0]]->{species}->[1]->{alignment_start};
  printf OUTFILE  "         <alignment_end>%d</alignment_end>\n", $probes->{probe}->[$index[$i][0]]->{species}->[1]->{alignment_end};
  printf OUTFILE  "         <alignment_strand>%s</alignment_strand>\n",$probes->{probe}->[$index[$i][0]]->{species}->[1]->{alignment_strand};
  printf OUTFILE  "         <chromosome>%s</chromosome>\n", $probes->{probe}->[$index[$i][0]]->{species}->[1]->{chromosome};
  printf OUTFILE  "         <probe_start>%d</probe_start>\n",$probes->{probe}->[$index[$i][0]]->{species}->[1]->{probe_start};
  printf OUTFILE  "         <probe_end>%d</probe_end>\n",$probes->{probe}->[$index[$i][0]]->{species}->[1]->{probe_end};
  printf OUTFILE  "         <sequence>%s</sequence>\n", $probes->{probe}->[$index[$i][0]]->{species}->[1]->{sequence};
  printf OUTFILE  "      </species>\n";
  printf OUTFILE  "   </probe>\n\n\n";  
}

close OUTFILE;


#########################################################################
# getParams - gets all options from the command line or keeps defaults
#             dies if required options are not included
#
#########################################################################
sub getParams {
    my %opts;
    my $errstr = "";
    use Getopt::Long;
    use Data::Dumper;
 
    GetOptions(\%opts, 'inputfile:s','outputfile:s', 'help');
     
    if ($opts{help})
    {
      $errstr = " ";
    }

    if ($errstr) {
        print <<"END_USAGE";
Description:

This script will take a XML probe document, and will sort the
probes based upon start bp location.

Usage: combine.pl -inputfile <filename> -outputfile <filename> [-help]


END_USAGE
        print "\n$errstr" if ($errstr);
        die("\n");
    }
    return (
            inputfile  => $opts{inputfile},
            outputfile => $opts{outputfile}
           );
}