Source of file PeffFastaEntry.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\Modification;

use pgb_liv\php_ms\Core\Entry\DatabaseEntry;

use pgb_liv\php_ms\Core\Gene;

use pgb_liv\php_ms\Core\Organism;

use pgb_liv\php_ms\Core\Database\DatabaseFactory;

use pgb_liv\php_ms\Reader\HupoPsi\PsiVerb;

/**

 * FASTA entry parser to map generic PEFF headers to protein elements

 *

 * @author Andrew Collins

 */

class PeffFastaEntry implements FastaInterface

{

    public static function parseIdentifier($identifier)

    {

        $matches = null;

        $isMatched = preg_match('/^(\w+):([\w-]+)$/', $identifier, $matches);

        if (! $isMatched) {

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

        }

        return array(

            $matches[1],

            $matches[2]

        );

    }

    /**

     *

     * {@inheritdoc}

     */

    public function getProtein($identifier, $description)

    {

        $protein = new Protein();

        // Parse identifier

        $identifierParts = $this->parseIdentifier($identifier);

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

        $dbEntry = new DatabaseEntry($database);

        $protein->setDatabaseEntry($dbEntry);

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

        // Parse description

        $matches = null;

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

        $attributes = array();

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

            $attributes[$key] = $matches[2][$index];

        }

        $this->parseAttributes($protein, $attributes);

        return $protein;

    }

    /**

     * Parses the attribute array and inputs the data into the protein

     *

     * @param Protein $protein

     *            Object to input values to

     * @param array $attributes

     *            Array to read from

     * @return void

     */

    private function parseAttributes(Protein $protein, array $attributes)

    {

        if (isset($attributes[PsiVerb::NCBI_TAX_ID])) {

            $organism = Organism::getInstance($attributes[PsiVerb::NCBI_TAX_ID]);

            $protein->setOrganism($organism);

        }

        if (isset($attributes[PsiVerb::TAX_NAME])) {

            if (! $protein->getOrganism()) {

                $protein->setOrganism(new Organism());

            }

            $protein->getOrganism()->setName($attributes[PsiVerb::TAX_NAME]);

        }

        foreach ($attributes as $key => $value) {

            switch ($key) {

                case 'DbUniqueId':

                    $protein->setAccession($value);

                    break;

                case 'GName':

                    $gene = Gene::getInstance($value);

                    $protein->setGene($gene);

                    break;

                case 'SV':

                    $protein->getDatabaseEntry()->setSequenceVersion($value);

                    break;

                case 'EV':

                    $protein->getDatabaseEntry()->setEntryVersion($value);

                    break;

                case 'PE':

                    $protein->getDatabaseEntry()->setEvidence($value);

                    break;

                case 'PName':

                    $protein->setDescription($value);

                    break;

                case 'ModRes':

                case 'ModResPsi':

                case 'ModResUnimod':

                    $modifications = self::parseModifications($value);

                    $protein->addModifications($modifications);

                    break;

                case PsiVerb::NCBI_TAX_ID:

                case PsiVerb::TAX_NAME:

                    // Safe to ignore - already handled

                    break;

                case 'Length':

                case 'VariantSimple ':

                case 'VariantComplex':

                case 'Processed':

                    // Not supported

                    break;

                default:

                    // Not supported

                    break;

            }

        }

    }

    /**

     * Parses ModResPsi/ModResUnimod element and returns the parsed modifications

     *

     * @param string $value

     *            The ModResXXX value

     * @return Modification[]

     */

    private static function parseModifications($value)

    {

        $modifications = array();

        $matches = null;

        preg_match_all('/\(([^()]|(?R))*\)/', $value, $matches);

        foreach ($matches[0] as $modString) {

            $elements = null;

            preg_match('/\(([0-9,]+)\|([A-Z]+:[0-9]+)?\|(.*)\|?(.+)?\)/', $modString, $elements);

            $locations = explode(',', $elements[1]);

            foreach ($locations as $location) {

                $modification = new Modification();

                $modification->setLocation((int) $location);

                $modification->setName($elements[3]);

                $modification->setAccession($elements[2]);

                $modifications[] = $modification;

            }

        }

        return $modifications;

    }

}