从模式中找到2个文件中的最长匹配

Question

我在此程序中执行两个文件时遇到问题。我正在尝试访问文件$Q和$s的内容。

print "Input the K value \n"; 
$k = <>; 
chomp $k; 

print "Input T\n"; 
$t = <>; 
chomp $t; 

%Qkmer =();      
$i = 1; 

$query=' '; 
while ($line=<IN>) { 
chomp($line); 
if ($line=~ m/^>/) { 
next; 
} 
$query=$query.$line; 
$line=~ s/(^|\n)[\n\s]*/$1/g; 

while (length($line) >= $k) { 
    $line =~ m/(.{$k})/; 
    if (! defined $Qkmer{$1}) {#every key not deined as the first match 
    $Qkmer{$1} = $i; 
    } 
    $i++; 
    $line = substr($line, 1, length($line) -1); 
} 
} 

open(MYDATA, '<', "data.txt"); 

while ($line=<MYDATA>) { \ 
    chomp($line); 
    %Skmer =();   # This initializes the hash called Skmer. 
    $j = 1; 

    if ($line=~ m/^>/) { #if the line starts with > 
    next; #start on next line #separated characters 
    } 
    $line=~ s/^\s+|\s+$//g ; #remove all spaces from file 
    while (length($line) >= $k) { 
    $line =~ m/(.{$k})/;#match any k characters and only k characters in dna 
    $Skmer{$1} = $j; #set the key position to $j and increase for each new key 
    $j++; 
    $line = substr($line, 1, length($line) -1); #this removes the first character in the current string 
    } 

    ###(56)###for($Skmerkey(keys %Skmer)){ 
    $i=$Skmer{$Skmerkey}; 
    if(defined $Qkmer($Skmerkey)){ 
     $j=$Qkmer($Skmerkey); 
     } 
     $S1=$line; 
     $S2=$query; 
     @arrayS1= split(//, $S1); 
     @array2= split(//, $S2); 

     $l=0; 
     while($arrayS1[$i-$l] eq $arrayS2[$j-$l]){ 
     $l++; 
     } 
     $start=$i-$l; 
     $m=0; 
     while ($arrayS1[$i+$k+$m] eq $arrayS2[$j+$k+$m]) { 
     $m++; 
     } 
     $length=$l+$k+$m; 
     $match= substr($S1, $start, $length); 

     if($length>$t){ 
     $longest=length($match); 
     print "Longest: $match of length $longest \n"; 
     } 
    } 

}###(83)### 

输入文件只包含字母串。例如：

文件1：

ahhtsagnchjgstffhjyfcsghnvzfhg 

文件2：

ggujvfbgfgkjfcijjjffcvvafcsghnvzfhgvugxckugcbhfcgh 
ghnvzfhgvugxckHhfgjgcfujvftjbvdtkhvddgjcdgjxdjkfrh 
ajdbvciyqdanvkjghnvzfhgvugxc 

从匹配文件2长度$k在文件1的单词的，我从检查在文件2中匹配词的左侧和右侧以进一步匹配。最终输出是基于$k的文件1和文件2之间最长的匹配。现在我GE

有了这个代码，我得到一个语法错误，为什么，因为它看起来是正确的给我我不发售者：

syntax error at testk.pl line 56, near "$Skmerkey(" 
syntax error at testk.pl line 83, near "}" 

谢谢。

Answer 1

use strict;   # <--- Allways use this 
use warnings;  # <--- and this 
use Data::Dumper; 

my $k=3; 

open(my $IN, '<', "File2"); # use $IN instead of depricated IN 
my $line=0; # line number 
my %kmer; # hash of arrays of all $k-letter "words" line/position 
my @Q;  # rows of Q-file 
while(<$IN>) { 
    chomp; 
    next if /^>/; 
    s/^\s+|\s+$//g; 
    next if !$_; 
    my $pos=0; 
    push @Q, $_; # store source row 
    for(/(?=(.{$k}))/g) { # Capture $k letters. floating window with step 1 symbol 
    push @{$kmer{$_}}, [$line,$pos]; # store row number and position of "word" 
    $pos++; 
    } 
    $line++; 
} 

open($IN, '<', "File1"); 
$line=0; 
while(<$IN>) { # Read S-file 
    chomp; 
    next if /^>/; 
    s/^\s+|\s+$//g; 
    next if !$_; 
    my $pos=0; 
    my $len=length($_); # length of row of S-file 
    my $s=$_;   # Current row of S-file 
    my @ignore=();  # array for store information about match tails 
    for(/(?=(.{$k}))/g) { 
    next if ! $kmer{$_}; # "word" not found try to next 
    for(@{$kmer{$_}}) { # $kmer{word} contains array of lines/positions in Q 
     my($qline, $qpos)=@{$_}; 
#  print "test $qline:$qpos "; 
     if(grep {$_->[0]==$qline && $_->[1]==$qpos } @ignore) { 
     # this line/position already tested and included in found matching 
#  print "Ignore match tail $qline:$qpos\n"; 
     next; 
     } 
     my $j=$k; # $k letters same, test after this point 
     my $qlen=length($Q[$qline]); 
     $j++ while($pos+$j<$len && $qpos+$j<$qlen && 
        substr($s,$pos+$j,1) eq substr($Q[$qline],$qpos+$j,1)); 
     print "MATCH FOUND: S-file line $line pos $pos, Q-file line $qline pos $qpos: ", 
      substr($s,$pos,$j),"\n"; 
     push @ignore, [$qline, $qpos, $j]; # store positions and length of match 
    } 
    } continue { # Continue block works on all loops, include after "next" 
    $pos++; 
    @ignore=grep { # recalculate/filter position and length of all match tails 
        ++$_->[1]; # increment position 
        (--$_->[2]) # decrement length 
        >= $k  # and filter out lengths < $k 
       } @ignore; 
# print Dumper(\@ignore); 
    } 
    $line++; 
}