“percent identity“的perl代码

计算单机版Blat的
    单机版Blat的匹配结果中没有percent identity（网络版的Blat输出结果中有）。为了筛选输出结果，常常需要计算每个匹配的percent identity；UCSC的Blat—FAQ中虽然给出了相应的解决办法（http://genome.ucsc.edu/FAQ/FAQblat#blat4），但其代码是用C写的，不利于使用Perl的生物信息学工作人员调用。此处给出相应的perl代码，如下所示（非原创，版权归原作者所有）：
while (<>) {
    chomp $_;
    my @v = split( /\t/, $_ );
    get_pid(@v);
}sub get_pid {
    my @line = @_;
    my $pid = ( 100.0 - ( &pslCalcMilliBad(@line) * 0.1 ) );
    print "The percentage: $pid\n";    #return $pid;
}sub pslCalcMilliBad {
    my @cols = @_;    # sizeNul depens of dna/Prot
    my $sizeMul = 1;    #if ($option{p}) {
    #        $sizeMul = 3;
    #} else {
    #        $sizeMul = 1;
    #}    # cols[0]  matches
    # cols[1]  misMatches
    # cols[2]  repMaches
    # cols[4]  qNumInsert
    # cols[6]  tNumInsert
    # cols[11] qStart
    # cols[12] qEnd
    # cols[15] tStart
    # cols[16] tEnd    my $qAliSize = $sizeMul * ( $cols[12] - $cols[11] );
    my $tAliSize = $cols[16] - $cols[15];    # I want the minimum of qAliSize and tAliSize
    my $aliSize;
    $qAliSize < $tAliSize ? $aliSize = $qAliSize : $aliSize = $tAliSize;    # return 0 is AliSize == 0
    return 0 if ( $aliSize <= 0 );    # size diff
    my $sizeDiff = $qAliSize - $tAliSize;
    if ( $sizeDiff < 0 ) {
        $sizeDiff = 0;        #if ($option{m}) {
        #$sizeDiff = 0;
        #} else {
        #$sizeDiff = -($sizeDiff);
        #}
    }    # insert Factor
    my $insertFactor = $cols[4];    #$insertFactor += $cols[6] unless ($option{m});
    my $milliBad = (
        1000 * (
            $cols[1] * $sizeMul +
              $insertFactor +
              &round( 3 * log( 1 + $sizeDiff ) )
        )
    ) / ( $sizeMul * ( $cols[0] + $cols[2] + $cols[1] ) );
    return $milliBad;}sub round {
    my $number = shift;
    return int( $number + .5 );
}