QueryDecipher.php

<?php

namespace App\Console\Commands;

use Illuminate\Console\Command;

use App\Decipher;
use App\Gene;

class QueryDecipher extends Command
{
    /**
     * The name and signature of the console command.
     *
     * @var string
     */
    protected $signature = 'decipher:query';

    /**
     * The console command description.
     *
     * @var string
     */
    protected $description = 'Command description';

    /**
     * Create a new command instance.
     *
     * @return void
     */
    public function __construct()
    {
        parent::__construct();
    }

    /**
     * Execute the console command.
     *
     * @return mixed
     */
    public function handle()
    {
		echo "Updating HI Predictions from Decipher ...";

		try {

			// $results = file_get_contents("https://decipher.sanger.ac.uk/files/downloads/HI_Predictions_Version3.bed.gz");
			$results = file_get_contents("https://www.deciphergenomics.org/files/downloads/HI_Predictions_Version3.bed.gz");

		} catch (\Exception $e) {

			echo "\n(E001) Error retreiving decipher data\n";
			exit;

		}

		// unzip the data
		$data = gzdecode($results);

		// discard the header
		$line = strtok($data, "\n");

		// parse the remaining file
		while (($line = strtok("\n")) !== false)
		{
			$parts = explode("\t", $line, 5);

			// what we want is in the fourth section...
			if (isset($parts[3]))
			{
				//... and is itself delimited by pipes
				$subparts = explode('|', $parts[3]);

				if (isset($subparts['2']) && strpos($subparts['2'], '%') !== false)
				{
					$gene = Gene::where('name', $subparts[0])->first();

					if (empty($gene))
					{
						// check previous sympols
						$gene = Gene::whereJsonContains('prev_symbol', $subparts[0])->first();
					}

					if (empty($gene))
						continue;

					// remove the percent sign
					$k = strpos($subparts['2'], '%');

					$gene->hi = substr($subparts['2'], 0, $k);
					$gene->save();
					// echo $subparts['0'] . " has a HI of " . $subparts['2'] . "\n";
				}
			}
		}

		echo "DONE\n";

    }
}