Source of file FastaWriter.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\Writer;

use pgb_liv\php_ms\Core\Protein;

use pgb_liv\php_ms\Reader\HupoPsi\PsiVerb;

/**

 * A file writer class for creating FASTA files.

 * Generates data in PEFF only.

 *

 * @author Andrew Collins

 */

class FastaWriter

{

    const DECOY_COUNT = '_DecoyCount';

    const UNKNOWN_PLACEHOLDER = 'Unknown';

    private $tmpHandle = null;

    private $outputHandle = null;

    private $databases = array();

    private $conversion = null;

    /**

     * Creates a new instance of a Fasta Writer.

     *

     * @param string $path

     *            The path to write data to

     */

    public function __construct($path)

    {

        $this->tmpHandle = tmpfile();

        $this->outputHandle = fopen($path, 'w');

    }

    public function write(Protein $protein)

    {

        if (is_null($this->tmpHandle)) {

            throw new \BadMethodCallException('File handle is not open, write cannot be called after close');

        }

        $this->writeDescription($protein);

        $this->writeSequence($protein);

    }

    public function close()

    {

        if (is_null($this->tmpHandle)) {

            return;

        }

        $this->writeHeader();

        fseek($this->tmpHandle, 0);

        while ($line = fgets($this->tmpHandle)) {

            fwrite($this->outputHandle, $line);

        }

        fclose($this->outputHandle);

        fclose($this->tmpHandle);

        $this->outputHandle = null;

        $this->tmpHandle = null;

    }

    public function __destruct()

    {

        $this->close();

    }

    private function writeHeader()

    {

        $header = '# PEFF 1.0' . PHP_EOL;

        $header .= '# GeneralComment=Generated by phpMs (http://pgb.liv.ac.uk/phpMs)' . PHP_EOL;

        $header .= '# //' . PHP_EOL;

        foreach ($this->databases as $prefix => $database) {

            if ($prefix == '') {

                continue;

            }

            $header .= '# Prefix=' . $prefix . PHP_EOL;

            if ($database[self::DECOY_COUNT] == $database[PsiVerb::NUMBER_OF_ENTRIES]) {

                $database['Decoy'] = 'true';

            } elseif ($database[self::DECOY_COUNT] == 0) {

                $database['Decoy'] = 'false';

            }

            unset($database[self::DECOY_COUNT]);

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

                $header .= '# ' . $key . '=' . $value . PHP_EOL;

            }

            if (! is_null($this->conversion)) {

                $header .= '# Conversion=Converted from ' . $this->conversion . PHP_EOL;

            }

            $header .= '# //' . PHP_EOL;

        }

        fwrite($this->outputHandle, $header);

    }

    private function writeDescription(Protein $protein)

    {

        $this->recordDatabase($protein);

        $description = '>' . $protein->getDatabaseEntry()

            ->getDatabase()

            ->getPrefix() . ':' . $protein->getDatabaseEntry()->getUniqueIdentifier();

        if ($protein->getDescription()) {

            $description .= ' \PName=' . $protein->getDescription();

        }

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

            $gene = $protein->getGene();

            if ($gene->getSymbol()) {

                $description .= ' \GName=' . $gene->getSymbol();

            }

        }

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

            $organism = $protein->getOrganism();

            if (! is_null($organism->getName())) {

                $description .= ' \\' . PsiVerb::TAX_NAME . '=' . $protein->getOrganism()->getName();

            }

            if (! is_null($organism->getIdentifier())) {

                $description .= ' \\' . PsiVerb::NCBI_TAX_ID . '=' . $protein->getOrganism()->getIdentifier();

            }

        }

        if ($protein->getDatabaseEntry()->getSequenceVersion()) {

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

        }

        if ($protein->getDatabaseEntry()->getEntryVersion()) {

            $description .= ' \EV=' . $protein->getDatabaseEntry()->getEntryVersion();

        }

        if ($protein->getDatabaseEntry()->getEvidence()) {

            $description .= ' \PE=' . $protein->getDatabaseEntry()->getEvidence();

        }

        $description .= ' \Length=' . $protein->getLength();

        fwrite($this->tmpHandle, $description);

    }

    private function writeSequence(Protein $protein)

    {

        fwrite($this->tmpHandle, PHP_EOL . wordwrap($protein->getSequence(), 60, PHP_EOL, true) . PHP_EOL);

    }

    private function recordDatabase(Protein $protein)

    {

        $database = $protein->getDatabaseEntry()->getDatabase();

        $prefix = $database->getPrefix();

        $this->initialiseDatabase($prefix);

        if ($this->databases[$prefix][PsiVerb::DB_NAME] == self::UNKNOWN_PLACEHOLDER && ! is_null($database->getName())) {

            $this->setHeader($prefix, PsiVerb::DB_NAME, $database->getName());

        }

        if ($this->databases[$prefix][PsiVerb::DB_SOURCE] == self::UNKNOWN_PLACEHOLDER &&

            ! is_null($database->getSource())) {

            $this->setHeader($prefix, PsiVerb::DB_SOURCE, $database->getSource());

        }

        $this->databases[$prefix][PsiVerb::NUMBER_OF_ENTRIES] ++;

        if ($protein->isDecoy()) {

            $this->databases[$prefix][self::DECOY_COUNT] ++;

        }

    }

    private function initialiseDatabase($prefix)

    {

        if (isset($this->databases[$prefix])) {

            return;

        }

        $this->databases[$prefix] = array();

        $this->databases[$prefix][PsiVerb::DB_NAME] = self::UNKNOWN_PLACEHOLDER;

        $this->databases[$prefix][PsiVerb::DB_VERSION] = self::UNKNOWN_PLACEHOLDER;

        $this->databases[$prefix][PsiVerb::DB_SOURCE] = self::UNKNOWN_PLACEHOLDER;

        $this->databases[$prefix][PsiVerb::SEQUENCE_TYPE] = 'AA';

        $this->databases[$prefix][PsiVerb::NUMBER_OF_ENTRIES] = 0;

        $this->databases[$prefix][self::DECOY_COUNT] = 0;

    }

    public function setHeader($prefix, $key, $value)

    {

        $this->initialiseDatabase($prefix);

        $this->databases[$prefix][$key] = $value;

    }

    public function setConversionSource($sourceFile)

    {

        $this->conversion = $sourceFile;

    }

    public function isConversion()

    {

        return $this->conversion;

    }

}