Perl递归技术？

Question

我需要一些关于这段代码的帮助。我知道应该递归的部分，或者至少我认为我知道但不确定如何实现它。我正在尝试从对齐矩阵实现路径查找程序，该程序将找到返回零值的多条路径。例如，如果您执行我的代码并插入 CGCA 作为第一个序列，CACGTAT 作为第二个序列，以及 1、0 和 -1 作为匹配、错配和空位分数。该程序给出了 HDHHDD 的路径和

的对齐方式

中美贸易协定

CGC--A-。

然而，除了我不知道有多少之外，还有更多可能的路径和对齐方式。我想要做的是让我的一段代码循环回到自身并找到其他路径和路线，使用与第一次相同的代码，直到它用完可能的路线。我在网上找到的最好的方法是递归，但没有人能解释如何去做。在这种情况下，应该还有两个路径和对齐方式:HDDDHHD 和 CACGTAT，以及 C--GCA- 和。 HDDDDHH、CACGTAT 和 --CGCA-。我只是不知道如何编写代码来执行此任务。

# Implementation of Needleman and Wunsch Algorithm

my($seq1, $len1, $seq2, $len2, $data, @matrix, $i, $j, $x, $y, $val1, $val2);
my($val3, $pathrow, $pathcol, $seq1loc, $seq2loc, $gapscore, $matchscore, $mismatchscore);

#first obtain the data from the user. 
print "Please enter the first sequence for comaprsion\n";
$seq1=<STDIN>;
chomp $seq1;

print "Please enter the second sequence for comparsion\n";
$seq2=<STDIN>;
chomp $seq2;


# adding extra characters so sequences align with matrix
# saves some calculations later on
$seq1 = " " . $seq1;
$seq2 = " " . $seq2;
$len1 = length($seq1);
$len2 = length($seq2);

print "Enter the match score: ";
$matchscore=<STDIN>;
chomp $matchscore;

print "Enter the mismatch score: ";
$mismatchscore=<STDIN>;
chomp $mismatchscore;

print "Enter the gap score: ";
$gapscore=<STDIN>;
chomp $gapscore;

# declare a two dimensional array and initialize to spaces
# array must contain one extra row and one extra column
@matrix = ();  
for($i = 0; $i < $len1; $i++){  
   for($j = 0; $j < $len2; $j++){  
      $matrix[$i][$j] = ' ';  
   }  
}  

# initialize 1st row and 1st column of matrix  
$matrix[0][0] = 0;  
for ($i = 1; $i < $len1; $i ++){  
    $matrix[$i][0] = $matrix[$i-1][0] + $gapscore;  
}  
for ($i = 1; $i < $len2; $i ++){  
    $matrix[0][$i] = $matrix[0][$i-1] + $gapscore;  
}  


# STEP 1:
# Fill in rest of matrix using the following rules:
# determine three possible values for matrix[x][y]
# value 1 = add gap score to matrix[x][y-1]
# value 2 = add gap score to matrix[x-1][y]
# value 3 = add match score or mismatch score to 
#           matrix[x-1][y-1] depending on nucleotide 
#           match for position x of $seq1 and position y
#           of seq2
# place the largest of the three values in matrix[x][y]
#
# Best alignment score appears in matrix[$len1][$len2].

for($x = 1; $x < $len1; $x++){  
   for($y = 1; $y < $len2; $y++){  
 $val1 = $matrix[$x][$y-1] + $gapscore;  
 $val2 = $matrix[$x-1][$y] + $gapscore;  
 if (substr($seq1, $x, 1) eq substr($seq2, $y, 1)){  
           $val3 = $matrix[$x-1][$y-1] + $matchscore;  
 }  
 else{  
    $val3 = $matrix[$x-1][$y-1] + $mismatchscore;  
 }  
 if (($val1 >= $val2) && ($val1 >= $val3)){  
    $matrix[$x][$y] = $val1;  
 }  
 elsif (($val2 >= $val1) && ($val2 >= $val3)){  
    $matrix[$x][$y] = $val2;  
 }  
 else{  
    $matrix[$x][$y] = $val3;  
 }  
   }  
}  

# Display scoring matrix  
print "MATRIX:\n";   
for($x = 0; $x < $len1; $x++){  
   for($y = 0; $y < $len2; $y++){  
 print "$matrix[$x][$y] ";  
   }  
   print "\n";  
}  
print "\n";    

# STEP 2:  
# Begin at matrix[$len1][$len2] and find a path to   
# matrix[0][0].  
# Build string to hold path pattern by concatenating either   
# 'H' (current cell produced by cell horizontally to left),   
# 'D' (current cell produced by cell on diagonal),   
# 'V' (current cell produced by cell vertically above)
# ***This is were I need help I need this code to be recursive, so I can find more then one path***

$pathrow = $len1-1;  
$pathcol = $len2-1;  

while (($pathrow != 0) || ($pathcol != 0)){  
    if ($pathrow == 0){  
       # must be from cell to left  
       $path = $path . 'H';  
       $pathcol = $pathcol - 1;  
    }  
    elsif ($pathcol == 0){  
       # must be from cell above  
       $path = $path . 'V';  
       $pathrow = $pathrow - 1;  
    }  
    # could be from any direction  
    elsif  (($matrix[$pathrow][$pathcol-1] + $gapscore) == $matrix[$pathrow][$pathcol]){  
       # from left  
       $path = $path . 'H';  
       $pathcol = $pathcol - 1;  
    }  
    elsif (($matrix[$pathrow-1][$pathcol] + $gapscore) == $matrix[$pathrow][$pathcol]){  
       # from above  
       $path = $path . 'V';  
       $pathrow = $pathrow - 1;  
    }   
    else{  
       # must be from diagonal  
       $path = $path . 'D';  
       $pathrow = $pathrow - 1;  
       $pathcol = $pathcol - 1;  
    }  


}   



print "Path is $path\n";   

# STEP 3:
# Determine alignment pattern by reading path string 
# created in step 2.
# Create two string variables ($alignseq1 and $alignseq2) to hold 
# the sequences for alignment.
# Reading backwards from $seq1, $seq2 and path string, 
#   if string character is 'D', then 
#      concatenate to front of $alignseq1, last char in $seq1 
#      and to the front of $alignseq2, last char in $seq2
#   if string character is 'V', then 
#      concatenate to front of $alignseq1, last char in $seq1 
#      and to the front of $alignseq2, the gap char
#   if string character is 'H', then 
#      concatenate to front of $alignseq1 the gap char
#      and to the front of $alignseq2, last char in $seq2
# Continue process until path string has been traversed.
# Result appears in string $alignseq1 and $seq2
***#I need this code to be recursive as well.***

$seq1loc = $len1-1;  
$seq2loc = $len2-1;  
$pathloc = 0;  
print length($path);  
while ($pathloc < length($path)){  
   if (substr($path, $pathloc, 1) eq 'D'){  
      $alignseq1 = substr($seq1, $seq1loc, 1) . $alignseq1;  
      $alignseq2 = substr($seq2, $seq2loc, 1) . $alignseq2;  
      $seq1loc--;  
      $seq2loc--;  
   }  
   elsif (substr($path, $pathloc, 1) eq 'V'){  
      $alignseq1 = substr($seq1, $seq1loc, 1) . $alignseq1;  
      $alignseq2 = '-' . $alignseq2;  
      $seq1loc--;  
   }    
   else{  # must be an H  
      $alignseq1 = '-' . $alignseq1;  
      $alignseq2 = substr($seq2, $seq2loc, 1) . $alignseq2;  
      $seq2loc--;  
   }    
   $pathloc++;  
}  

print "\nAligned Sequences:\n";  
print "$alignseq2 \n";  
print "$alignseq1 \n";  

# statement may be needed to hold output screen  
print "Press any key to exit program";  
$x = <STDIN>;   

如果有人想知道这是一个 needleman-wunsch 算法。我们将不胜感激。

Answer 1

我无法提供答案，因为我不明白你到底想做什么，但我可以提供一些一般性建议。

开始将您的代码组织成执行狭义定义任务的离散子例程。此外，实现中央算法的子程序不应面向从键盘接收输入并向屏幕产生输出；相反，他们应该接收输入作为参数并返回结果。如果需要用户输入或屏幕输出，这些任务应该放在单独的子例程中，而不是与您的主要算法混合在一起。

沿着这条路走下去的第一步(也是部分)是带你整个程序，把它包含在一个子例程定义中，然后用所需的参数调用子例程。子例程不应打印其关键结果，而应返回它们——具体来说，是对 @matrix 的引用以及 $path 的值, $alignseq1 , $alignseq2 .

sub NW_algo {
    my ($seq1, $seq2, $matchscore, $mismatchscore, $gapscore) = @_;

    # The rest of your code here, but with all print
    # statements and <STDIN> inputs commented out.

    return \@matrix, $path, $alignseq1, $alignseq2;
}

my(@return_values) = NW_algo('CGCA', 'CACGTAT', 1, 0, -1);

Print_matrix($return_values[0]);

sub Print_matrix {
    for my $m ( @{$_[0]} ){
        print join(' ', @$m), "\n";
    }
}

此时，您将拥有一个可以被其他代码调用的算法，从而可以更轻松地测试和调试您的程序。例如，您可以定义各种输入数据集并运行 NW_algo()在每组。只有这样，才有可能考虑递归或其他技术。