perl - Finding longest match between 2 files from pattern -

i having trouble implementing 2 files within program. trying to access contents of file $q , $s.

print "input 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 first match      $qkmer{$1} = $i;    }    $i++;    $line = substr($line, 1, length($line) -1);  } }  open(mydata, '<', "data.txt");  while ($line=<mydata>) { \   chomp($line);   %skmer = ();           # initializes hash called skmer.   $j = 1;    if ($line=~ m/^>/ ) { #if line starts >     next; #start on next line #separated characters   }   $line=~ s/^\s+|\s+$//g ; #remove spaces file   while (length($line) >= $k) {     $line =~ m/(.{$k})/;#match k characters , k characters in dna     $skmer{$1} = $j; #set key position $j , increase each new key     $j++;     $line = substr($line, 1, length($line) -1); #this removes first character in current string   }    ###(56)###for($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)### 

the input files contain strings of letters. example:

file 1:

ahhtsagnchjgstffhjyfcsghnvzfhg 

file2:

ggujvfbgfgkjfcijjjffcvvafcsghnvzfhgvugxckugcbhfcgh ghnvzfhgvugxckhhfgjgcfujvftjbvdtkhvddgjcdgjxdjkfrh ajdbvciyqdanvkjghnvzfhgvugxc 

from match of word of length$k in file 1 in file 2, check match in file 2 left , right of word further matches. final output longest match between file 1 , file 2 based on $k. ge

with code, syntax error , not suer why because looks correct me:

syntax error @ testk.pl line 56, near "$skmerkey(" syntax error @ testk.pl line 83, near "}"   

thank you.

use strict;         # <--- allways use use warnings;       # <--- , use data::dumper;  $k=3;  open(my $in, '<', "file2");  # use $in instead of depricated in $line=0;  # line number %kmer;    # hash of arrays of $k-letter "words" line/position @q;       # rows of q-file while(<$in>) {   chomp;   next if /^>/;      s/^\s+|\s+$//g;    next if !$_;   $pos=0;   push @q, $_;    # store source row   for(/(?=(.{$k}))/g) {  # capture $k letters. floating window step 1 symbol    push @{$kmer{$_}}, [$line,$pos];  # store row number , position of "word"    $pos++;   }   $line++; }  open($in, '<', "file1"); $line=0; while(<$in>) {   # read s-file   chomp;   next if /^>/;   s/^\s+|\s+$//g;   next if !$_;   $pos=0;   $len=length($_);  # length of row of s-file   $s=$_;            # current row of s-file   @ignore=();       # array store information match tails   for(/(?=(.{$k}))/g) {     next if ! $kmer{$_};  # "word" not found try 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 ) {       # line/position tested , included in found matching #        print "ignore match tail $qline:$qpos\n";         next;       }       $j=$k;  # $k letters same, test after point       $qlen=length($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 , length of match     }   } continue {  # continue block works on loops, include after "next"    $pos++;    @ignore=grep { # recalculate/filter position , length of match tails                   ++$_->[1];  # increment position                   (--$_->[2]) # decrement length                    >= $k      # , filter out lengths < $k                 } @ignore; #   print dumper(\@ignore);   }   $line++; }