└── convert.php


/convert.php:
--------------------------------------------------------------------------------
  1 | <?php
  2 | class Resources {
  3 |     public $_genetic_map = array(  );
  4 |     public $_genetic_map_name = "";
  5 |     public $_cytoBand_hg19 = array(  );
  6 |     public $_knownGene_hg19 = array(  );
  7 |     public $_kgXref_hg19 = array(  );
  8 |     public $resources_dir="";
  9 |     function __construct(){
 10 |         $this->_genetic_map = array(  );
 11 |         $this->_genetic_map_name = "";
 12 |         $this->_cytoBand_hg19 = array(  );
 13 |         $this->_knownGene_hg19 = array(  );
 14 |         $this->_kgXref_hg19 = array(  );
 15 |         $this->resources_dir="resources";
 16 |     }
 17 |     public function  _load_genetic_map_HapMapII_GRCh37($filename){
 18 |         $genetic_map = array(  );
 19 |         $archive = new PharData($filename);
 20 |         foreach($archive as $file) {
 21 |             if (strpos("genetic_map",$file["name"])===true){
 22 |                 $df = array(  );
 23 |                 if (($handle = fopen($file, "r")) !== FALSE) {
 24 |                     while (($data = fgetcsv($handle,"\t")) !== FALSE) {
 25 |                         $df["Position(bp)"]=$data["pos"];
 26 |                         $df["Rate(cM/Mb)"]=$data["rate"];
 27 |                         $df["Map(cM)"]=$data["map"];
 28 |                     }
 29 |                     fclose($handle);
 30 |                 }
 31 |                 $start_pos = strpos($file["name"],"chr") + 3;
 32 |                 $end_pos = strpos($file["name"],".");
 33 |                 $genetic_map[substr($file["name"],$start_pos,$end_pos)] = $df;
 34 |             }
 35 |         }
 36 |         $genetic_map["X"] = array_merge(
 37 |             $genetic_map["X_par1"], $genetic_map["X"], $genetic_map["X_par2"]
 38 |         );
 39 |         $genetic_map["X_par1"]=array( );
 40 |         $genetic_map["X_par2"]=array( );
 41 |         return $genetic_map;
 42 |     } 
 43 |     
 44 |     public function _download_file($url, $filename, $compress=False, $timeout=30){
 45 |         if(strpos($url, "ftp://") !== false) {
 46 |             $url=str_replace($url,"ftp://", "http://");
 47 |         } 
 48 |         if ($compress && substr($filename,strlen($filename)-3,strlen($filename)) != ".gz"){
 49 |             $filename = $filename+".gz";
 50 |         }
 51 |         $destination = join($this->resources_dir, $filename);
 52 | 
 53 |         if (!mkdir($destination)){
 54 |             return "";
 55 |         }
 56 |         if (file_exists($destination)){            
 57 |             $file_url = $destination;
 58 |             header('Content-Type: application/octet-stream');
 59 |             header('Content-Description: File Transfer');
 60 |             header('Content-Disposition: attachment; filename=' . $filename);
 61 |             header('Expires: 0');
 62 |             header('Cache-Control: must-revalidate');
 63 |             header('Pragma: public');
 64 |             header('Content-Length: ' . filesize($file_url));
 65 |             readfile($file_url);
 66 | 
 67 |             // if $compress
 68 |             //     $this->_write_data_to_gzip(f, data)
 69 |             // else
 70 |             //     f.write(data)           
 71 |         }   
 72 |         return $destination;
 73 |     }
 74 |     
 75 |     
 76 |     public function get_all_resources(){
 77 |         $resources = array( );
 78 |         $resources[
 79 |             "genetic_map_HapMapII_GRCh37"
 80 |         ] = $this->get_genetic_map_HapMapII_GRCh37();
 81 |         $resources["cytoBand_hg19"] = $this->get_cytoBand_hg19();
 82 |         $resources["knownGene_hg19"] = $this->get_knownGene_hg19();
 83 |         $resources["kgXref_hg19"] = $this->get_kgXref_hg19();
 84 |         return $resources;
 85 |     }
 86 |     public function download_example_datasets(){
 87 |         return [
 88 |             $this->_download_file(
 89 |                 "https://opensnp.org/data/662.23andme.340",
 90 |                 "662.23andme.340.txt.gz",
 91 |                 $compress=True
 92 |             ),
 93 |             $this->_download_file(
 94 |                 "https://opensnp.org/data/662.ftdna-illumina.341",
 95 |                 "662.ftdna-illumina.341.csv.gz",
 96 |                 $compress=True
 97 |             ),
 98 |             $this->_download_file(
 99 |                 "https://opensnp.org/data/663.23andme.305",
100 |                 "663.23andme.305.txt.gz",
101 |                 $compress=True
102 |             ),
103 |             $this->_download_file(
104 |                 "https://opensnp.org/data/4583.ftdna-illumina.3482",
105 |                 "4583.ftdna-illumina.3482.csv.gz"
106 |             ),
107 |             $this->_download_file(
108 |                 "https://opensnp.org/data/4584.ftdna-illumina.3483",
109 |                 "4584.ftdna-illumina.3483.csv.gz"
110 |             ),
111 |         ];
112 |     }
113 | }
114 |  
115 | ?>
116 |        


--------------------------------------------------------------------------------