Source of file MsgfPlusSearch.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\Search;

use pgb_liv\php_ms\Search\Parameters\SearchParametersInterface;

use pgb_liv\php_ms\Search\Parameters\MsgfPlusSearchParameters;

/**

 * Client to perform MS-GF+ search and results retrieval

 *

 * @author Andrew Collins

 */

class MsgfPlusSearch

{

    private $exePath;

    private $javaPath;

    private $host = null;

    /**

     * Create a new instance of this class.

     * Must supply server details.

     *

     * @param string $exePath

     *            Path to the MSGFPlus.jar executable

     * @param string $javaPath

     *            Path to the JRE executable

     */

    public function __construct($exePath, $javaPath = 'java')

    {

        $this->exePath = $exePath;

        $this->javaPath = $javaPath;

    }

    /**

     * Execute the command on the target host via SSH

     *

     * @param string $host

     */

    public function setHost($host)

    {

        $this->host = $host;

    }

    /**

     * Perform the MS-GF+ search using the specified parameters.

     * Any paramaters not specified will use the MS-GF+ defaults.

     *

     * @param SearchParametersInterface $parameters

     *            Paramaters object for any arguments to send to MS-GF+

     * @throws \InvalidArgumentException Thrown if any of the required properties are missing

     * @return string Path to the results file

     */

    public function search(SearchParametersInterface $parameters)

    {

        if (! is_a($parameters, 'pgb_liv\php_ms\Search\Parameters\MsgfPlusSearchParameters')) {

            throw new \InvalidArgumentException('Argument 1 expected to be of type MsgfPlusSearchParameters');

        }

        if (is_null($parameters->getSpectraPath()) || ! file_exists($parameters->getSpectraPath())) {

            throw new \InvalidArgumentException('Valid Spectra file must be specified in paramaters.');

        }

        if (is_null($parameters->getDatabases()) || ! file_exists($parameters->getDatabases())) {

            throw new \InvalidArgumentException('Valid database file must be specified in paramaters.');

        }

        $command = $this->getCommand($parameters);

        $this->executeCommand($command);

        if (! is_null($parameters->getOutputFile())) {

            return $parameters->getOutputFile();

        } else {

            $extensionPos = strrpos($parameters->getSpectraPath(), '.');

            return substr($parameters->getSpectraPath(), 0, $extensionPos) . '.mzid';

        }

    }

    private function getCommand(MsgfPlusSearchParameters $parameters)

    {

        $command = $this->javaPath;

        $command .= ' -jar ';

        $command .= $this->exePath;

        $command .= ' -s "' . $parameters->getSpectraPath() . '"';

        $command .= ' -d "' . $parameters->getDatabases() . '"';

        $command .= $this->appendArgument(' -o', $parameters->getOutputFile());

        if (! is_null($parameters->getPrecursorTolerance())) {

            $command .= ' -t ' . $parameters->getPrecursorTolerance()->getTolerance() .

                 $parameters->getPrecursorTolerance()->getUnit();

        }

        $command .= $this->appendArgument(' -ti', $parameters->getIsotopeErrorRange());

        $command .= $this->appendArgument(' -thread', $parameters->getNumOfThreads());

        $command .= $this->appendArgument(' -tda', $parameters->isDecoyEnabled() ? 1 : 0);

        $command .= $this->appendArgument(' -m', $parameters->getFragmentationMethodId());

        $command .= $this->appendArgument(' -inst', $parameters->getMs2DetectorId());

        $command .= $this->appendArgument(' -e', $parameters->getEnzyme());

        $command .= $this->appendArgument(' -protocol', $parameters->getProtocolId());

        $command .= $this->appendArgument(' -ntt', $parameters->getTolerableTrypticTermini());

        if (! is_null($parameters->getModificationFile())) {

            $command .= ' -mod ' . $parameters->getModificationFile();

        } elseif (count($parameters->getModifications()) > 0) {

            $path = MsgfPlusSearchParameters::createModificationFile($parameters->getModifications());

            $command .= ' -mod "' . $path . '"';

        }

        $command .= $this->appendArgument(' -minLength', $parameters->getMinPeptideLength());

        $command .= $this->appendArgument(' -maxLength', $parameters->getMaxPeptideLength());

        $command .= $this->appendArgument(' -minCharge', $parameters->getMinPrecursorCharge());

        $command .= $this->appendArgument(' -maxCharge', $parameters->getMaxPrecursorCharge());

        $command .= $this->appendArgument(' -n', $parameters->getNumMatchesPerSpectrum());

        $command .= $this->appendArgument(' -addFeatures', $parameters->getAdditionalFeatures());

        $command .= $this->appendArgument(' -ccm', $parameters->getChargeCarrierMass());

        $command .= $this->appendArgument(' -showQValue', $parameters->getShowQValue());

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

            $command = 'ssh ' . $this->host . ' "' . addslashes($command) . '"';

        }

        return $command;

    }

    private function appendArgument($key, $value)

    {

        if (is_null($value)) {

            return '';

        }

        return $key . ' ' . $value;

    }

    /**

     * Executes the MSGF+ Command.

     *

     * @param string $command

     *            Complete command line argument to execute

     * @throws \InvalidArgumentException Thrown if MS-GF+ writes anything to stderr

     * @return string Path to MS-GF+ stdout log file

     */

    private function executeCommand($command)

    {

        $stdoutPath = tempnam(sys_get_temp_dir(), 'php-msMsgfOut');

        $stderrPath = tempnam(sys_get_temp_dir(), 'php-msMsGfErr');

        $descriptors = array(

            0 => array(

                'pipe',

                'r'

            ),

            1 => array(

                'file',

                $stdoutPath,

                'a'

            ),

            2 => array(

                'file',

                $stderrPath,

                'a'

            )

        );

        $process = proc_open($command, $descriptors, $pipes);

        proc_close($process);

        if (filesize($stderrPath) > 0) {

            throw new \InvalidArgumentException(file_get_contents($stderrPath));

        }

        return $stdoutPath;

    }

}