Source of file ProBedWriter.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\Entry\ProteinEntry;

use pgb_liv\php_ms\Core\Spectra\PrecursorIon;

use pgb_liv\php_ms\Core\Identification;

use pgb_liv\php_ms\Core\Peptide;

/**

 * A file writer class for creating proBed files.

 *

 * @author Andrew Collins

 */

class ProBedWriter

{

    private $fileHandle = null;

    private $name;

    private $uniqueId = 0;

    /**

     * Creates a new instance of a ProBed Writer.

     *

     * @param string $path

     *            The path to write data to

     */

    public function __construct($path, $name, array $headers = array())

    {

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

        $this->name = $name;

        $this->writeHeader($headers);

    }

    public function write(PrecursorIon $spectra)

    {

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

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

        }

        foreach ($spectra->getIdentifications() as $identification) {

            $this->writeIdentification($spectra, $identification);

        }

    }

    public function close()

    {

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

            fclose($this->fileHandle);

            $this->fileHandle = null;

        }

    }

    public function __destruct()

    {

        $this->close();

    }

    private function writeHeader(array $headers)

    {

        fwrite($this->fileHandle, '# proBed-version' . "\t" . '1.0' . PHP_EOL);

        fwrite($this->fileHandle, '# Created on ' . date('r') . ' by phpMs' . PHP_EOL);

        foreach ($headers as $header) {

            fwrite($this->fileHandle, '# ' . $header . PHP_EOL);

        }

    }

    private function writeIdentification(PrecursorIon $spectra, Identification $identification)

    {

        $peptide = $identification->getPeptide();

        if ($peptide->isDecoy()) {

            return;

        }

        foreach ($peptide->getProteins() as $proteinEntry) {

            // Verify suitable for output

            if (! $this->isValid($proteinEntry)) {

                continue;

            }

            $protein = $proteinEntry->getProtein();

            $minStart = min($proteinEntry->getChromosomePositionsStart());

            $relPositions = array();

            foreach ($proteinEntry->getChromosomePositionsStart() as $position) {

                $relPositions[] = $position - $minStart;

            }

            $relPositions = implode(',', $relPositions);

            // chrom

            fwrite($this->fileHandle, $protein->getChromosome()->getName() . "\t");

            // chromStart

            fwrite($this->fileHandle, ($minStart - 1) . "\t");

            // chromEnd

            fwrite($this->fileHandle, ($proteinEntry->getChromosomePositionEnd() + 1) . "\t");

            // name

            fwrite($this->fileHandle, ($protein->getAccession() . '_' . $this->uniqueId) . "\t");

            // score

            fwrite($this->fileHandle, '1000' . "\t");

            // strand

            fwrite($this->fileHandle, $protein->getChromosome()->getStrand() . "\t");

            // thickStart

            fwrite($this->fileHandle, ($minStart - 1) . "\t");

            // thickEnd

            fwrite($this->fileHandle, ($proteinEntry->getChromosomePositionEnd() + 1) . "\t");

            // reserved

            fwrite($this->fileHandle, '0' . "\t");

            // blockCount

            fwrite($this->fileHandle, $proteinEntry->getChromosomeBlockCount() . "\t");

            // blockSizes

            fwrite($this->fileHandle, implode(',', $proteinEntry->getChromosomeBlockSizes()) . "\t");

            // chromStarts

            fwrite($this->fileHandle, $relPositions . "\t");

            // proteinAccession

            fwrite($this->fileHandle, $protein->getAccession() . "\t");

            // peptideSequence

            fwrite($this->fileHandle, $peptide->getSequence() . "\t");

            // uniqueness

            fwrite($this->fileHandle, (count($peptide->getProteins()) == 1 ? 'unique' : 'not-unique[unknown]') . "\t");

            // genomeReferenceVersion

            fwrite($this->fileHandle,

                (is_null($protein->getChromosome()->getGenomeReferenceVersion()) ? '.' : $protein->getChromosome()->getGenomeReferenceVersion()) .

                "\t");

            // TODO: psmScore

            fwrite($this->fileHandle, '.' . "\t");

            // fdr

            fwrite($this->fileHandle, $identification->getScore('MS:1002356') . "\t");

            // modifications

            fwrite($this->fileHandle, $this->getModificationString($peptide) . "\t");

            // charge

            fwrite($this->fileHandle, $spectra->getCharge() . "\t");

            // expMassToCharge

            fwrite($this->fileHandle, $spectra->getMassCharge() . "\t");

            // calcMassToCharge

            fwrite($this->fileHandle, $peptide->getMonoisotopicMassCharge($spectra->getCharge()) . "\t");

            // psmRank

            fwrite($this->fileHandle, $identification->getRank() . "\t");

            // datasetID

            fwrite($this->fileHandle, $this->name . "\t");

            // uri - not implementable?

            fwrite($this->fileHandle, '.' . "\n");

            $this->uniqueId ++;

        }

    }

    private function getModificationString(Peptide $peptide)

    {

        $mods = array();

        foreach ($peptide->getModifications() as $modification) {

            $modStr = $modification->getLocation() . '-';

            if (is_null($modification->getAccession())) {

                // Spec states mass value should be specified?

                $modStr = 'MS:1001460';

            } else {

                $modStr .= $modification->getAccession();

            }

            $mods[] = $modStr;

        }

        return count($mods) > 0 ? implode(',', $mods) : '.';

    }

    private function isValid(ProteinEntry $proteinEntry)

    {

        if (! is_a($proteinEntry, '\pgb_liv\php_ms\Core\ProteinEntry\ChromosomeProteinEntry')) {

            return false;

        }

        $protein = $proteinEntry->getProtein();

        $chromosome = $protein->getChromosome();

        // Possible unmapped protein

        // TODO: Correct handling missing version. Required by spec?

        // if (is_null($chromosome) || is_null($chromosome->getGenomeReferenceVersion())) {

        if (is_null($chromosome)) {

            return false;

        }

        return true;

    }

}