#!/usr/bin/perl

use strict;
use Data::Dumper;


require XML::Simple;

my %params = getParams();
my $xml_file = new XML::Simple();
my $probes = $xml_file->XMLin($params{file}, keyattr => {});

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



#########################################################################
# 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, 'file=s','base=s');
    if ($opts{help})
    {
      $errstr = " ";
    }

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

This script will assign a "temp" name to each probe in the XML file based
upon the base name given on the command line.

Usage: name_probes.pl -file <name> -base <base_probename>

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