Source of file EnsembleFastaEntry.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\Entry\DatabaseEntry;

use pgb_liv\php_ms\Core\Gene;

use pgb_liv\php_ms\Core\Protein;

use pgb_liv\php_ms\Core\Chromosome;

use pgb_liv\php_ms\Core\Transcript;

use pgb_liv\php_ms\Core\Database\EnsembleGDatabase;

use pgb_liv\php_ms\Core\Database\EnsembleTDatabase;

use pgb_liv\php_ms\Core\Database\DatabaseFactory;

/**

 * FASTA entry parser to map Ensemble header to protein elements

 *

 * @author Andrew Collins

 */

class EnsembleFastaEntry implements FastaInterface

{

    const CHROMOSOME = 'chromosome';

    const GENE = 'gene';

    const GENE_BIOTYPE = 'gene_biotype';

    const GENE_SYMBOL = 'gene_symbol';

    const TRANSCRIPT = 'transcript';

    const TRANSCRIPT_BIOTYPE = 'transcript_biotype';

    const DESCRIPTION = 'description';

    public static function parseIdentifier($identifier)

    {

        $matches = null;

        $isMatched = preg_match('/^(ENSP|GENSCAN)([0-9]+).([0-9]+)$/', $identifier, $matches);

        if (! $isMatched) {

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

        }

        return array(

            $matches[1],

            $matches[2],

            $matches[3]

        );

    }

    /**

     *

     * {@inheritdoc}

     */

    public function getProtein($identifier, $description)

    {

        $protein = new Protein();

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

        $dbEntry = null;

        $database = DatabaseFactory::getDatabase($identifierParts[0]);

        $dbEntry = new DatabaseEntry($database);

        $protein->setDatabaseEntry($dbEntry);

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

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

        $matches = array();

        preg_match_all('/(\w+):(.*?(?=\s\[|\s\w+:))/', $description, $matches);

        $keyValues = array();

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

            switch ($value) {

                case self::CHROMOSOME:

                case self::GENE:

                case self::GENE_BIOTYPE:

                case self::GENE_SYMBOL:

                case self::TRANSCRIPT:

                case self::TRANSCRIPT_BIOTYPE:

                case self::DESCRIPTION:

                    $keyValues[$value] = $matches[2][$key];

                    break;

                default:

                    // Unknown

                    break;

            }

        }

        if (isset($keyValues[self::CHROMOSOME])) {

            $chromosome = new Chromosome();

            $chromosome->setName($keyValues[self::CHROMOSOME]);

            $protein->setChromosome($chromosome);

        }

        if (isset($keyValues[self::GENE])) {

            if (isset($keyValues[self::GENE_SYMBOL])) {

                $gene = Gene::getInstance($keyValues[self::GENE_SYMBOL]);

            } else {

                $gene = new Gene();

            }

            $geneEntry = new DatabaseEntry(EnsembleGDatabase::getInstance());

            $geneEntry->setUniqueIdentifier($keyValues[self::GENE]);

            $gene->setDatabaseEntry($geneEntry);

            $protein->setGene($gene);

            if (isset($keyValues[self::GENE_BIOTYPE])) {

                $gene->setType($keyValues[self::GENE_BIOTYPE]);

            }

        }

        if (isset($keyValues[self::TRANSCRIPT])) {

            $transcript = new Transcript();

            $transcriptEntry = new DatabaseEntry(EnsembleTDatabase::getInstance());

            $transcriptEntry->setUniqueIdentifier($keyValues[self::TRANSCRIPT]);

            $transcript->setDatabaseEntry($transcriptEntry);

            $protein->setTranscript($transcript);

            if (isset($keyValues[self::TRANSCRIPT_BIOTYPE])) {

                $transcript->setType($keyValues[self::TRANSCRIPT_BIOTYPE]);

            }

        }

        if (isset($keyValues[self::DESCRIPTION])) {

            $protein->setDescription($keyValues[self::DESCRIPTION]);

        }

        return $protein;

    }

}