Dear PerlMonks

I am trying to selectively color a sequence of 100 characters and writing a html file.I have written the code and but its somewhat too many loops and is giving some errors.

I was wondering if I get some suggestions in troubleshooting and reducing the code

.

Error: In the output, position number 11 (T). I am also trying to color the last 10 characters as blue instead of red.

Any help will be greatly appreciated.
Regards 


#!/usr/bin/perl
use strict;
use warnings;
use LWP::Simple;
use Data::Dumper;

my $sequence="GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCC
+CGAGGCTCCGCACCAGCCGCGCTTCTGTCCGCCTGCAGGGCATT";

############ Make array of rejected length ###############
my $seqlen = length ($sequence);
my $input = "fragments.txt";
open(K,">","temp_hash.txt");
open( my $infile, "<", $input ) || die "Check the $input $!\n";
my $old = 0;
while ( my $line = <$infile> ){
    my $gap = $line - $old;
    if ($gap > 2){
    my $start = $old+1;
        my $end = $line-1;
        print K "$start\t$end\n"; 
    }
    elsif ($gap == 2){
        my $start = $old+1;
        print K "$start\t$start\n"; 
    }
    $old = $line;
}
close ($infile);

my $line = $seqlen+1;
my $gap = $line - $old;
if ($gap > 2){
    my $start = $old+1;
    my $end = $line-1;
    print K "$start\t$end\n"; 
}
elsif ($gap == 2){
    my $start = $old+1;
    print K "$start\t$start\n"; 
}
close (K); close ($infile);


####################### Make a Hash ########################

my $tempfile = "temp_hash.txt";
open(my $file, "<", $tempfile) or die "Check the file $!";
my $cnt = 1;my %split;
while (my $line = <$file>){
    chomp $line;
    if ($line =~/(\S+)\s+(\S+)/){
        for (my $s=$1;$s<=$2;$s++){
            push @{$split{$cnt}}, $s;
        }
    }
    $cnt++;
}
close ($file); 

############# Write HTML file #############################
#my $header;
open(AA, ">fragments.html") or die $!;
print AA "<!DOCTYPE html PUBLIC \"-\/\/W3C\/\/DTD XHTML 1.0 Strict\/\/
+EN\" \"http:\/\/www.w3.org\/TR\/xhtml1\/DTD\/xhtml1-strict.dtd\">\n";
print AA "<html xmlns=\"http:\/\/www.w3.org\/1999\/xhtml\" lang=\"en\"
+ xml:lang=\"en\">\n";
print AA "<head>\n";
print AA "<title> Colored Gene Walk</title> <meta http-equiv=\"content
+-type\" content=\"text/html;charset=utf-8\"/>\n";
print AA "</head>\n";
print AA "<body>\n";
print AA "<pre class=\"monofont\">\n";
print AA "<a style=\"font-size: 12pt\">\n";
#print AA "$header\n";

for (my $pos=1;$pos<=length($sequence);$pos++){
    my $FLAG=0;my @temp=();
    foreach my $k(sort {$a <=> $b} keys %split){
        my @pos=@{$split{$k}};
        my $p1 =$pos[0];
        my $p2 =$pos[$#pos];
        if($pos == $p1){
            push (@temp, "<span style=\"color:red\">");
            for(my $p=$p1;$p<=$p2;$p++){
                my $s=substr($sequence,$p-1,1);
                push (@temp,$s);
                if($p==int($p/50)*50){
                    push (@temp,"<br />");
                }
                $FLAG=1; $pos++;
            }
            push (@temp, "</span>");
        }
    }
    if($FLAG ==0){
        my $s=substr($sequence,$pos-1,1);
        print AA "$s";
    }
    else{
        printf AA join("",@temp);
    }
    if($pos==int($pos/50)*50){
       printf  AA "<br />";
    }
}

print AA "\n";
print AA "</a>\n";
print AA "</pre>\n";
print AA "</body>\n";
print AA "</html>\n";

close (AA);

[download]
fragments.txt
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
51
52
53
54
55
56
57
58
59
60
86
87
88
89
90
91
92
93
94
95

[download]

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