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perl script for overlap algo

i've written the following code for overlap algo but its not giving me an output please help me

perl script for overlap algorithm

#!/usr/bin/perl              
%gencode =
      (TTT => "F", TTC => "F", TTA => "L", TTG => "L",
      TCT => "S", TCC => "S", TCA => "S", TCG => "S",
      TAT => "Y", TAC => "Y", TAA => "*", TAG => "*",
      TGT => "C", TGC => "C", TGA => "*", TGG => "W",
      CTT => "L", CTC => "L", CTA => "L", CTG => "L",
      CCT => "P", CCC => "P", CCA => "P", CCG => "P",
      CAT => "H", CAC => "H", CAA => "Q", CAG => "Q",
      CGT => "R", CGC => "R", CGA => "R", CGG => "R",
      ATT => "I", ATC => "I", ATA => "I", ATG => "M",
      ACT => "T", ACC => "T", ACA => "T", ACG => "T",
      AAT => "N", AAC => "N", AAA => "K", AAG => "K",
      AGT => "S", AGC => "S", AGA => "R", AGG => "R",
      GTT => "V", GTC => "V", GTA => "V", GTG => "V",
      GCT => "A", GCC => "A", GCA => "A", GCG => "A",
      GAT => "D", GAC => "D", GAA => "E", GAG => "E",
      GGT => "G", GGC => "G", GGA => "G", GGG => "G" );
      # The BLOSUM62 amino acid substitution matrix  
%blosum62 =
     #  A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V
   ( [  4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0],  # A
     [ -1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3],  # R
     [ -2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3],  # N
     [ -2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3],  # D
     [  0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1],  # C
     [ -1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2],  # Q
     [ -1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2],  # E
     [  0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3],  # G
     [ -2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3],  # H
     [ -1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3],  # I
     [ -1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1],  # L
     [ -1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2],  # K
     [ -1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1],  # M 
     [ -2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1],  # F
     [ -1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2],  # P
     [  1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2],  # S
     [  0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0],  # T
     [ -3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3],  # W
     [ -2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1],  # Y
     [  0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4]);   # V
     #A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V      
     # The amino acids, and a hashmap from amino acid to its index 0-19  

my $seq1 = "MSTYLNFAAPPPP"; 
my $seq2 = "MSIRYLNPAAK";  
# scoring scheme 
 $gap = -8;  
# initialization 
my @matrix; 
$matrix[0][0]{score}   = 0; 
$matrix[0][0]{pointer} = "none"; 
for( $j = 1; $j <= length($seq1); $j++) {
     $matrix[0][$j]{score}   = 0;
     $matrix[0][$j]{pointer} = "none";
 } 
for ( $i = 1; $i <= length($seq2); $i++) {
     $matrix[$i][0]{score}   = 0;
     $matrix[$i][0]{pointer} = "none"; 
}  
# fill 
$max_i     = 0; 
$max_j     = 0; 
$max_score = 0; 
$scoring_matrix = $blosum62; 
for( $i = 1; $i <= length($seq2); $i++) {
     for( $j = 1; $j <=length($seq1);$j++) {
             $max_i     = $i;
             $max_j     = $j;
             $max_score = $matrix[$i][$j]{score};
         }
     }

# trace-back  
 $align1 = ""; 
 $align2 = "";  
 $j = $max_j; 
 $i = $max_i;  
while (1) {
     last if $matrix[$i][$j]{pointer} eq "none";
     if ($matrix[$i][$j]{pointer} eq "diagonal") {
         $align1 .= substr($seq1, $j-1, 1);
         $align2 .= substr($seq2, $i-1, 1);
         $i--; $j--;
     }elsif ($matrix[$i][$j]{pointer} eq "left") {
         $align1 .= substr($seq1, $j-1, 1);
         $align2 .= "-";
         $j-$gap;
     }elsif($matrix[$i][$j]{pointer} eq "up"){
         $align1 .= "-";
         $align2 .= substr($seq2, $i-1, 1);
         $i-$gap;
     }
}  
$align1 = reverse $align1; 
$align2 = reverse $align2; 
print "$align1"; 
print "$align2"; 
print "&poa ,$align1, $align2";  

sub poa {

    $matches = 0;
     @seq1 = ($seq1);
     @seq2 = ($seq2);
     for($i = 0; $i <= $seq1 ; $i++) {
          if($seq1[$i] eq $seq2[$i]){
               $matches++;
         }
     }
     return $matches;
}
perl alignment algorithm overlap
• 2,902 views • link
updated by Michael Dondrup Michael Dondrup • written by zunaira.ehsan21 • zunaira.ehsan21

What a mess~

Nobody will help you unless you format the code. Learn more about the markdown format.

• 0 views • link
written by shenwei356 shenwei356

2 answers

I agree @shenwei356! On top of that it's PERL, on top of that no documentation/ comments! It seems impossible to understand what's going on (after few weeks/months) even for the person who wrote it!!

• 0 views • link
written by lakhujanivijay lakhujanivijay

The first line of the script is missing the #. It should be

#!/usr/bin/perl

If you add the lines 

use strict;
use warnings;

after the first line of the script, it will give you useful error messages, and point out what lines have problems with syntax, etc.

If 'score' and 'pointer' are variables, then they should be preceded by a $, plus they don't seem to be defined anywhere in the script.

In the subroutine poa, I assume you want to split the string $seq1 into individual characters and store them in the array. The way to do this in perl is

my @seq1 = split(//, $seq1);
• 0 views • link
updated by Ram Ram • written by mastal511 mastal511

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