<?php
define("CGI_DIR","/var/www/cgi-bin/");
define("GENEPHP_DIR","/var/www/cgi-bin/GENEPHP/");
define("TMP_DIR","/tmp/");


//to parse the spidey result
include(GENEPHP_DIR . 'parsers/spidey.inc.php');
//to create my sequence object
include(GENEPHP_DIR . 'parsers/fasta.inc.php');
include_once(GENEPHP_DIR . 'seqIOexport.inc.php');
//to generate my image
include(GENEPHP_DIR . 'biograph/seqDraw.inc.php');

include(GENEPHP_DIR . 'genephp.inc.php');

/*
 *create a seq object with the genomic sequence of interest (my source is locuslink)
 */

$parser=new seqIOimport(TMP_DIR . "genomic.fa", 'fasta');

if ($parser) {
   while (!$parser->eof()) {
        $s=$parser->fetch();
        $parser->Move_Next();
   }
}

/*
 * I execute SPIDEY, parse the result and add the mRNA features to my sequence object
 * for that I used as input genomic.fa and for instance refseq.fa
 * repbase is a fasta file with repeat sequence that has been formatted with formatdb
 */
$mrna_features = array();

exec(CGI_DIR . 'spidey.linux -i ' . TMP_DIR . 'genomic.fa -m ' . TMP_DIR . 'refseq.fa -p 0 -o ' . TMP_DIR . 'resultatspidey -R ' . CGI_DIR . 'repbase');


$fh_spidey    = fopen(TMP_DIR . "resultatspidey", r);
    
$importer     = new parse_spidey($fh_spidey);
        
while(!feof($importer->source)) {
    $f = $importer->fetchNext();
}

$mrna_features[] = $importer->mrna_features;

$s->features[mRNA] = $mrna_features;

/*
 * I draw my pics
 *
 *
 */

$panel1 = new panel(
array(
        'length'             => $s->seqlength,
        'start'              => 0,
        'stop'               => $s->seqlength,
        'pad_top'            => 20,
        'pad_bottom'         => 20,
        'pad_left'           => 40,
        'pad_right'          => 40,
        'width'              => 900,
        'spacebetweentracks' => 30
    )
);


$panel1->add_track(
    array(
        'type'  => 'text',
        'color' => 'red',
        'text'  => 'Genomic annotation of PAK1',
        'position' =>'center'
    )
);


$panel1->add_track(
    array(
        'type'  => 'scale',
        'color' => 'black'
    )
);

$panel1->add_track(
    array(
        'type'                     => 'sequence',
        'color'                    => 'blue',
        'first_description'        => 'Chromosome ',
        'color_first_description'  => 'black',
        'second_description'       =>  $s->accession,
        'color_second_description' => 'cyan'
        
    )
);

$panel1->add_track(
    array(
        'type'  => 'text',
        'color' => 'blue',
        'text'  => 'Just one refseq for the BioPHP group ;-)',
        'position' =>'left'
    )
);

if (isset($s->features[mRNA])) {
    foreach($s->features[mRNA] as $mrna) {
        $panel1->add_track(
            array(
                'type'            => 'mRNA',
                'location'        => $mrna[location],
                'location_color'  => green,
                'location_link'   => FALSE,
                'accession'       => $mrna[acc],
                'accession_color' => 'cyan',
                'accession_link'  => FALSE,
                'strand'          => $mrna[strand],
                'spidey'          => TRUE
            )
        );
    }
}

$panel1->gd(TMP_DIR . "PAK1.png");


?>