Source of file UniProtFastaEntry.php

<?php

/**

 * Copyright 2019 University of Liverpool

 *

 * Licensed under the Apache License, Version 2.0 (the "License");

 * you may not use this file except in compliance with the License.

 * You may obtain a copy of the License at

 *

 * http://www.apache.org/licenses/LICENSE-2.0

 *

 * Unless required by applicable law or agreed to in writing, software

 * distributed under the License is distributed on an "AS IS" BASIS,

 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

 * See the License for the specific language governing permissions and

 * limitations under the License.

 */

namespace pgb_liv\php_ms\Reader\FastaEntry;

use pgb_liv\php_ms\Core\Protein;

use pgb_liv\php_ms\Core\Entry\DatabaseEntry;

use pgb_liv\php_ms\Core\Organism;

use pgb_liv\php_ms\Core\Gene;

use pgb_liv\php_ms\Core\Database\UniProtSpDatabase;

use pgb_liv\php_ms\Core\Database\UniProtTrDatabase;

/**

 * FASTA entry parser to map UniProt header to protein elements

 *

 * @author Andrew Collins

 */

class UniProtFastaEntry implements FastaInterface

{

    public static function parseIdentifier($identifier)

    {

        $matches = null;

        $isMatched = preg_match('/^(sp|tr)\|(\w+)\|(\w+)$/', $identifier, $matches);

        if (! $isMatched) {

            throw new \InvalidArgumentException($identifier . ' is not UniProt format');

        }

        return array(

            $matches[1],

            $matches[2],

            $matches[3]

        );

    }

    /**

     *

     * {@inheritdoc}

     */

    public function getProtein($identifier, $description)

    {

        // Parse identifier

        $identifierParts = self::parseIdentifier($identifier);

        $protein = new Protein();

        $dbEntry = null;

        if ($identifierParts[0] == 'sp') {

            $dbEntry = new DatabaseEntry(UniProtSpDatabase::getInstance());

        } elseif ($identifierParts[0] == 'tr') {

            $dbEntry = new DatabaseEntry(UniProtTrDatabase::getInstance());

        }

        $protein->setDatabaseEntry($dbEntry);

        $dbEntry->setUniqueIdentifier($identifierParts[1]);

        $dbEntry->setName($identifierParts[2]);

        // Parse description

        $osPosition = strpos($description, ' OS=');

        $protein->setDescription(substr($description, 0, $osPosition));

        $matches = array();

        preg_match_all('/(\w{2})=([\w\s]+)(?![\w=])/', $description, $matches);

        $keyValues = array();

        foreach ($matches[1] as $key => $value) {

            switch ($value) {

                case 'OS':

                case 'OX':

                case 'GN':

                case 'PE':

                case 'SV':

                    $keyValues[$value] = trim($matches[2][$key]);

                    break;

                default:

                    // Unknown

                    break;

            }

        }

        if (isset($keyValues['OX'])) {

            $organism = Organism::getInstance($keyValues['OX']);

            $protein->setOrganism($organism);

            if (isset($keyValues['OS'])) {

                $organism->setName($keyValues['OS']);

            }

        }

        if (isset($keyValues['GN'])) {

            $gene = Gene::getInstance($keyValues['GN']);

            $protein->setGene($gene);

        }

        if (isset($keyValues['PE'])) {

            $dbEntry->setEvidence($keyValues['PE']);

        }

        if (isset($keyValues['SV'])) {

            $dbEntry->setSequenceVersion($keyValues['SV']);

        }

        return $protein;

    }

}