perl script for overlap algo
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Entering edit mode
4.8 years ago

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 • 1.8k views
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2
Entering edit mode

What a mess~

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Entering edit mode
4.8 years ago

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!!

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Entering edit mode
4.8 years ago
mastal511 ★ 2.1k

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);
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