Matrix plot help

utterlyconfused has asked for the wisdom of the Perl Monks concerning the following question:

Hi I have the code below working. I now need to set a threshold for how many mis-matches can be tolerated and also set a user-provided limit for how many characters are matched at a time (i.e. matches groups of characters rather than one character at a time).
The two strings are being read in from separate files and compared and a dot printed for each matching group.
. I'm a perl beginner and I've tried combinations of pattern matches but with little success. I would appreciate any help in what to change in the code in order to achieve this/

#!/usr/bin/perl
use strict;use warnings;
my $i;my $j;my $a;
open (FH1,'<', "./CAM3UCA.txt");
open (FH2,'<', "./TCH3A.txt");
my $seq1 = do { local $/; <FH1> };
my $seq2 = do { local $/; <FH2> };

my @s1=split('',$seq1);
my @s2=split('',$seq2);
my @matrix=();

for($i=0;$i<scalar(@s2);$i++)
{
 for($j=0;$j<scalar(@s1);$j++)
 {
  if($s2[$i] eq $s1[$j])
  {
  $matrix[$i][$j]=".";
  }
  else
  {
  $matrix[$i][$j]=" ";
  }

 }
}

#Printing matrix of dot plot
open (FHOUT,">dotplot.txt") or die "cannot open outfile\n";
print FHOUT " ";
for($a=0;$a<scalar(@s1);$a++)
    {
print FHOUT "$s1[$a]";
}
print FHOUT "\n";
#print FHOUT "\n\n";
for($i=0;$i<scalar(@s2);$i++)
{
    print FHOUT "$s2[$i]";

 for($j=0;$j<scalar(@s1);$j++)
 {

print FHOUT "$matrix[$i][$j]";
 }
  print FHOUT "\n";
#print FHOUT "\n\n";
}

close FH1;
close FH2;
close FHOUT;<br>
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Re: Matrix plot help by wind (Priest) on Feb 15, 2011 at 21:02 UTC
This is what I interpret as the intention of your code, after a little cleaning up. Maybe it will help: #!/usr/bin/perl use strict; use warnings; my $seq1 = readfile("./CAM3UCA.txt"); my $seq2 = readfile("./TCH3A.txt"); my @s1 = split '', $seq1; my @s2 = split '', $seq2; my @matrix = (); for my $i (0..$#s2) { for my $j (0..$#s1) { $matrix[$i][$j] = $s2[$i] eq $s1[$j] ? '.' : " "; } } # Printing matrix of dot plot my $outfile = 'dotplot.txt'; open my $oh, '>', $outfile or die "Can't open file, $outfile: $!"; print $oh join('', @s1) . "\n"; print $oh join('', @s2) . "\n"; foreach my $row (@matrix) { print $oh join('', @$row) . "\n"; } close $oh; sub readfile { my $file = shift; open my $fh, $file or die "Can't open file, $file: $!"; local $/; <$fh>; } [download]	[reply] [d/l]

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Re: Matrix plot help
by wind (Priest) on Feb 15, 2011 at 21:02 UTC

#!/usr/bin/perl
use strict;
use warnings;

my $seq1 = readfile("./CAM3UCA.txt");
my $seq2 = readfile("./TCH3A.txt");

my @s1 = split '', $seq1;
my @s2 = split '', $seq2;

my @matrix = ();

for my $i (0..$#s2) {
    for my $j (0..$#s1) {
        $matrix[$i][$j] = $s2[$i] eq $s1[$j] ? '.' : " ";
    }
}

# Printing matrix of dot plot
my $outfile = 'dotplot.txt';
open my $oh, '>', $outfile or die "Can't open file, $outfile: $!";

print $oh join('', @s1) . "\n";
print $oh join('', @s2) . "\n";

foreach my $row (@matrix) {
    print $oh join('', @$row) . "\n";
}

close $oh;

sub readfile {
    my $file = shift;
    open my $fh, $file or die "Can't open file, $file: $!";
    local $/;
    <$fh>;
}
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