[PERL] Compare two sequences from fasta file

[frenchcookie]

Hello !

I would like to compare sequences that I have in one file. The most important think to me is that I would like to compare them in columns, so first position form sequence A with first position in sequence B etc.

Do you have any idea how to start?
(of course I don't expect prepared code, but maybe someone do something like this and could help me start )

This is how I start but it's give me error That file cannot be read.

my $end = $#a1 < $#a2 ? $#a1 : $#a2; 
 my $result = 0; 
 for (my $l=0; $l<=$end; $l++) { 
  $result++ if $a1[$l] eq $a2[$l];  
 } 
 
 my $A = (2 * $result) / ($#a1 + $#a2 + 2); 
 my $B = $result / ($end+1); 
 print "Similar = $result, A = $A, B = $B\n"; 
} 
 
  
my $file = 'seqs.txt';  
open I, '<', $file 
or die "Can't open '$file' for reading: $!\n"; 
  
chop (%hash = map { split /\s*,\s*/,$_,2 } grep (!/^$/,<I>)); 
 
 
 
 print "$_$hash{$_}\n" for keys %hash; 
open  
open (IN, $ARGV[0]) || die "File not found $ARGV[0]: $!\n"; 
chomp(my @in = <IN>); 
 
 
map { 
  s/[^agtc]//ig; 
} @in; 
 
 
my $dna1 = read_file($ARGV[0]); 
my $dna2 = read_file($ARGV[1]); 
compare ($dna1, $dna2); 
 
compare($in[0], $in[1]); 
compare($in[1], $in[2]); 
compare($in[2], $in[3]); 
 
close (IN);

[Apexy]

Hi Frenchcookie,

Could ask your question with and example? Such as the nature of your files and what you want the output to look like. Such as it is with the case here

HTH

[Jetse]

Do you mean something like this?

open( my $fh "filename.txt" )or die $!;
my @lines = <FILE>;
while ( <FILE> ) { print $_; 
  my @columns = split(separatorBetweenColumns,$_);
  my @splittedA = split('',$columns[0]);
  my @splittedB = split('',$columns[1]);
  for(my $i = 0; $i < @splittedA; $i++){
    if($splittedA[$i] eq $splittedB[$i]){
      #chars are equal...
    }
  }
}
close( $fh )

didn't test it, but this is a way to do it...

[Apexy]

Hello,

Without knowing what the inputs looks like, I will not know if the variables of your script is (scalar or string). If your files have columns, are they tab delimited? What should the script do if first position from sequence A matches with first position in sequence B? Simply put, the question is not clear to me.