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GlobalAlignment.pl
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GlobalAlignment.pl
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#!perl
use warnings;
use strict;
my @array;
my $sequences = <STDIN>;
chomp ($sequences);
open STDIN, "<$sequences" or die "Fein el-sequence el-awalany da yabni ?\n";
my @sequence1;
my @sequence2;
my $line;
my $count=0;
my $match = 5;
my $miss = -4;
my $gap = -5;
while (defined ($line = <STDIN>)){
chomp ($line);
push @array,$line;
$count++;
if($count==2){
last;
}
}
$sequence1[0]="";
$sequence2[0]="";
for(my $i=1;$i<=length($array[0]);$i++){
$sequence1[$i]=substr($array[0],$i-1,1);
}
for(my $i=1;$i<=length($array[1]);$i++){
$sequence2[$i]=substr($array[1],$i-1,1);
}
my @matrixValues;
my %hash;
#index 0 for i
$matrixValues [0][0][0] = 0;
#index 1 for j
$matrixValues [0][0][1] = 0;
#index 2 for score
$matrixValues [0][0][2] = 0;
my $d=0;
my $h=0;
my $v=0;
for(my $i=0;$i<@sequence1;$i++){ #vertical
for(my $j=0;$j<@sequence2;$j++){ #horizontal
if($i==0 and $j==0){
# print $i . "\t". $j . "\n";
# print $matrixValues [$i][$j][0]."\t";
# print $matrixValues [$i][$j][1]."\t";
# print $matrixValues [$i][$j][2]."\n";
next;
}
elsif($i==0){
$matrixValues [$i][$j][0]=$i;
$matrixValues [$i][$j][1]=$j-1;
$matrixValues [$i][$j][2]=$matrixValues [$i][$j-1][2]+$gap;
# print $i . "\t". $j . "\n";
# print $matrixValues [$i][$j][0]."\t";
# print $matrixValues [$i][$j][1]."\t";
# print $matrixValues [$i][$j][2]."\n";
}
elsif($j==0){
$matrixValues [$i][$j][0]=$i-1;
$matrixValues [$i][$j][1]=$j;
$matrixValues [$i][$j][2]=$matrixValues [$i-1][$j][2]+$gap;
# print $i . "\t". $j . "\n";
# print $matrixValues [$i][$j][0]."\t";
# print $matrixValues [$i][$j][1]."\t";
# print $matrixValues [$i][$j][2]."\n";
}
else {
$h=$matrixValues [$i][$j-1][2]+$gap;
$v=$matrixValues [$i-1][$j][2]+$gap;
if($sequence1[$i] eq $sequence2[$j]){
$d= $matrixValues [$i-1][$j-1][2]+$match;
}
else{
$d= $matrixValues [$i-1][$j-1][2]+$miss;
}
# if($i==52 and $j==54){
# print $matrixValues [$i-1][$j-1][2]."\n";
# print $d."\n".$v."\n".$h."\n";
# }
if($h>=$d and $h>=$v){
$matrixValues [$i][$j][0] = $i;
$matrixValues [$i][$j][1] = $j-1;
$matrixValues [$i][$j][2] = $h;
}
elsif($v>=$d and $v>=$h){
$matrixValues [$i][$j][0] = $i-1;
$matrixValues [$i][$j][1] = $j;
$matrixValues [$i][$j][2] = $v;
}
elsif($d>=$h and $d>=$v){
$matrixValues [$i][$j][0] = $i-1;
$matrixValues [$i][$j][1] = $j-1;
$matrixValues [$i][$j][2] = $d;
}
# print $i . "\t". $j . "\n";
# print $matrixValues [$i][$j][0]."\t";
# print $matrixValues [$i][$j][1]."\t";
# print $matrixValues [$i][$j][2]."\n";
# print $d."\n".$v."\n".$h."\n";
} #else
} #loop
} #loop
# print $matrixValues [@sequence1-1][@sequence2-1][0]."\n";
# print $matrixValues [@sequence1-1][@sequence2-1][1]."\n"; #53
# print $matrixValues [@sequence1-1][@sequence1-1][2]."\n"; #55
# print @sequence1."\t".@sequence2."\n";
# # print $sequence1[45]."\n";
my $i=@sequence1-1;
my $j=@sequence2-1;
my @newSeq1;
my @newSeq2;
my $x;
my $y;
while($i != 0 or $j != 0){
$x=$matrixValues[$i][$j][0];
$y=$matrixValues[$i][$j][1];
if($i-$x==1 and $j-$y==1){
unshift @newSeq1,$sequence1[$i];
unshift @newSeq2,$sequence2[$j];
# print $newSeq1[$i]."\t".$newSeq2[$j]."\n";
}
elsif($i-$x==0){
unshift @newSeq1,"-";
unshift @newSeq2,$sequence2[$j];
# print $newSeq1[$i]."\t".$newSeq2[$j]."\n";
}
elsif($j-$y==0){
unshift @newSeq1,$sequence1[$i];
unshift @newSeq2,"-";
# print $newSeq1[$i]."\t".$newSeq2[$j]."\n";
}
#print $newSeq1[$i]."\t".$newSeq2[$j]."\n";
$i=$x;
$j=$y;
}
# print @newSeq1-1 ."\n".@newSeq2-1 ."\n";
foreach my $seq1 (@newSeq1){
print $seq1;
}
print "\n";
foreach my $seq (@newSeq2){
print $seq;
}
print "\n"."Score: $matrixValues[@sequence1-1][@sequence2-1][2]". "\n";