sequence.php

#!/usr/bin/php
<?php
interface IFilter {
    public function bAccept($sSequence);
}

class CFilterRegExp implements IFilter {
    private $sRegExp;

    public function __construct($sRegExp)
    {
        $this->sRegExp = $sRegExp;
    }

    public function bAccept($sSequence) {
        return preg_match($this->sRegExp, $sSequence) > 0;
    }
}

class CRead {
    private $m_iSequenceLength;
    private $m_iOutputCountMax;
    private $m_oFilter;
    private $m_asiSequenceCount = [];

    public function __construct($iSequenceLength, $iOutputCount, IFilter $oFilter)
    {
        $this->m_iSequenceLength = $iSequenceLength;
        $this->m_iOutputCountMax = $iOutputCount;
        $this->m_oFilter           = $oFilter;
    }

    public function vReadFile($rFile) {
        while (($sLine = fread($rFile, 1024)) !== FALSE) {
            for ($iPosition = 0, $iLineLength = mb_strlen($sLine); $iPosition < $iLineLength; ++$iPosition) {
                $sSequence = mb_substr($sLine, $iPosition, $this->m_iSequenceLength);

                if ($this->m_oFilter->bAccept($sSequence) !== TRUE) {
                    continue;
                }

                if (!isset($this->m_asiSequenceCount[$sSequence])) {
                    $this->m_asiSequenceCount[$sSequence] = 0;
                }

                $this->m_asiSequenceCount[$sSequence]++;
            }

            if (feof($rFile)) {
                break;
            }
        }
    }

    public function tsGetReport() {
        arsort($this->m_asiSequenceCount, SORT_NUMERIC);

        $iOutputCount = 0;

        foreach ($this->m_asiSequenceCount as $sSequence => $iCount) {
            yield $sSequence . ' ' . $iCount;

            ++$iOutputCount;

            if ($this->m_iOutputCountMax <= $iOutputCount) {
                break;
            }
        }
    }
}

$oRead = new CRead(3, 10, new CFilterRegExp('~^\w+$~'));
$oRead->vReadFile(STDIN);
foreach ($oRead->tsGetReport() as $sReport) {
    echo $sReport . PHP_EOL;
}

exit(0);