如何将其更改为“惯用的" Perl? [英] How do I change this to "idiomatic" Perl?

问题描述

我开始更深入地研究Perl，但是在编写"Perl-ly"代码而不是在Perl中编写C时遇到了麻烦.如何更改以下代码以使用更多Perl习惯用法，我应该如何学习习惯用法?

I am beginning to delve deeper into Perl, but am having trouble writing "Perl-ly" code instead of writing C in Perl. How can I change the following code to use more Perl idioms, and how should I go about learning the idioms?

仅对其操作做一个解释:该例程是比对DNA或氨基酸序列的模块的一部分(如果您关心此类事情，请使用Needelman-Wunch).它创建了两个二维数组，一个数组用于存储两个序列中每个位置的分数，另一个数组用于跟踪路径，以便以后可以重新创建得分最高的对齐方式.效果很好，但是我知道我做的事情不是很简洁明了.

Just an explanation of what it is doing: This routine is part of a module that aligns DNA or amino acid sequences(using Needelman-Wunch if you care about such things). It creates two 2d arrays, one to store a score for each position in the two sequences, and one to keep track of the path so the highest-scoring alignment can be recreated later. It works fine, but I know I am not doing things very concisely and clearly.

编辑:这是一项作业.我完成了，但是想稍微整理一下我的代码.有关实现该算法的详细信息，可以在课程网站上中找到你们中的任何一个都感兴趣.

edit: This was for an assignment. I completed it, but want to clean up my code a bit. The details on implementing the algorithm can be found on the class website if any of you are interested.

sub create_matrix {
    my $self = shift;
    #empty array reference
    my $matrix = $self->{score_matrix};
    #empty array ref
    my $path_matrix = $self->{path_matrix};
    #$seq1 and $seq2 are strings set previously
    my $num_of_rows = length($self->{seq1}) + 1;
    my $num_of_columns = length($self->{seq2}) + 1;

    #create the 2d array of scores
    for (my $i = 0; $i < $num_of_rows; $i++) {
        push(@$matrix, []);
        push(@$path_matrix, []);
        $$matrix[$i][0] = $i * $self->{gap_cost};
        $$path_matrix[$i][0] = 1;
    }

    #fill out the first row
    for (my $i = 0; $i < $num_of_columns; $i++) {
        $$matrix[0][$i] = $i * $self->{gap_cost};
        $$path_matrix[0][$i] = -1;
    }
    #flag to signal end of traceback
    $$path_matrix[0][0] = 2;
    #double for loop to fill out each row
    for (my $row = 1; $row < $num_of_rows; $row++) {
        for (my $column = 1; $column < $num_of_columns; $column++) {
            my $seq1_gap = $$matrix[$row-1][$column] + $self->{gap_cost};
            my $seq2_gap = $$matrix[$row][$column-1] + $self->{gap_cost};
            my $match_mismatch = $$matrix[$row-1][$column-1] + $self->get_match_score(substr($self->{seq1}, $row-1, 1), substr($self->{seq2}, $column-1, 1));
            $$matrix[$row][$column] = max($seq1_gap, $seq2_gap, $match_mismatch);

            #set the path matrix
            #if it was a gap in seq1, -1, if was a (mis)match 0 if was a gap in seq2 1
            if ($$matrix[$row][$column] == $seq1_gap) {
                $$path_matrix[$row][$column] = -1;
            }
            elsif ($$matrix[$row][$column] == $match_mismatch) {
                $$path_matrix[$row][$column] = 0;
            }
            elsif ($$matrix[$row][$column] == $seq2_gap) {
                $$path_matrix[$row][$column] = 1;
            }
        }
    }
}

推荐答案

我也有其他一些评论，但这是第一个观察结果:

I have some other comments as well, but here is the first observation:

my $num_of_rows = length($self->{seq1}) + 1;
my $num_of_columns = length($self->{seq2}) + 1;

所以$self->{seq1}和$self->{seq2}是字符串，并且您继续使用substr访问单个元素.我希望将它们存储为字符数组:

So $self->{seq1} and $self->{seq2} are strings and you keep accessing individual elements using substr. I would prefer to store them as arrays of characters:

$self->{seq1} = [ split //, $seq1 ];

这就是我的写法:

sub create_matrix {
    my $self = shift;

    my $matrix      = $self->{score_matrix};
    my $path_matrix = $self->{path_matrix};

    my $rows = @{ $self->{seq1} };
    my $cols = @{ $self->{seq2} };

    for my $row (0 .. $rows) {
        $matrix->[$row]->[0] =  $row * $self->{gap_cost};
        $path_matrix->[$row]->[0] = 1;
    }

    my $gap_cost = $self->{gap_cost};

    $matrix->[0] = [ map { $_ * $gap_cost } 0 .. $cols ];
    $path_matrix->[0] = [ (-1) x ($cols + 1) ];

    $path_matrix->[0]->[0] = 2;

    for my $row (1 .. $rows) {
        for my $col (1 .. $cols) {
            my $gap1 = $matrix->[$row - 1]->[$col] + $gap_cost;
            my $gap2 = $matrix->[$row]->[$col - 1] + $gap_cost;
            my $match_mismatch =
                $matrix->[$row - 1]->[$col - 1] +
                $self->get_match_score(
                    $self->{seq1}->[$row - 1],
                    $self->{seq2}->[$col - 1]
                );

            my $max = $matrix->[$row]->[$col] =
                max($gap1, $gap2, $match_mismatch);

            $path_matrix->[$row]->[$col] = $max == $gap1
                    ? -1
                    : $max == $gap2
                    ? 1
                    : 0;
            }
        }
    }

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