Source of file UniprotFastaEntry.php

<?php

/**

 * Copyright 2016 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\Core\Database\Fasta;

use pgb_liv\php_ms\Core\Protein;

/**

 * A sequence Database Entry object.

 * By default the identifier, description

 * and sequence are available. Additional fields will be available if the

 * description has been able to be parsed in the case of FASTA data.

 *

 * @author Andrew Collins

 */

class UniprotFastaEntry extends DefaultFastaEntry implements FastaInterface

{

    /**

     *

     * {@inheritdoc}

     *

     * @see \pgb_liv\php_ms\Core\Database\Fasta\DefaultFastaEntry::getDescription()

     */

    public function getDescription(Protein $protein)

    {

        $description = '>' . $protein->getUniqueIdentifier();

        $description .= ' ' . $protein->getName();

        $description .= ' OS=' . $protein->getOrganismName();

        if (! is_null($protein->getGeneName())) {

            $description .= ' GN=' . $protein->getGeneName();

        }

        $description .= ' PE=' . $protein->getProteinExistence();

        return $description . ' SV=' . $protein->getSequenceVersion();

    }

    /**

     *

     * {@inheritdoc}

     *

     * @see \pgb_liv\php_ms\Core\Database\Fasta\DefaultFastaEntry::getProtein()

     */

    public function getProtein($identifier, $description, $sequence)

    {

        // Parse identifier

        $identifierParts = explode('|', $identifier, 3);

        $protein = new Protein();

        $protein->setSequence($sequence);

        $protein->setUniqueIdentifier($identifier);

        if (count($identifierParts) == 3) {

            $protein->setDatabasePrefix($identifierParts[0]);

            $protein->setAccession($identifierParts[1]);

            $protein->setEntryName($identifierParts[2]);

        } else {

            $protein->setAccession($identifierParts[0]);

            $protein->setEntryName($identifierParts[1]);

        }

        $protein->setDescription($description);

        // Parse description

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

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

        $matches = array();

        preg_match_all('/([OS|GN|PE|SV]{2})=(.+?(?=\s(GN=|PE=|SV=)|$))/', $description, $matches);

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

            if ($value == 'OS') {

                $protein->setOrganismName($matches[2][$key]);

            } elseif ($value == 'GN') {

                $protein->setGeneName($matches[2][$key]);

            } elseif ($value == 'PE') {

                $protein->setProteinExistence($matches[2][$key]);

            } elseif ($value == 'SV') {

                $protein->setSequenceVersion($matches[2][$key]);

            }

        }

        return $protein;

    }

}