#!/usr/bin/perl
use strict;
use warnings;
use LWP::Simple;
use Data::Dumper;
my $sequence="GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACCAGCCGCGCTTCTGTCCGCCTGCAGGGCATT";
############ Make hash of rejected length ###############
my $input = "fragments.txt";
my %split;
open (my $infile, "<", $input) or die "Cannot open file '$input' for reading: $!";
build_hash($_) while <$infile>;
close ($infile) or die "Cannot close file '$input': $!";
build_hash(length($sequence) + 1);
sub build_hash{
use feature 'state';
state $old = 0;
state $cnt = 1;
my ($line) = @_;
my $gap = $line - $old;
my $start = $old + 1;
my $end = ($gap > 2) ? $line - 1 : $start;
$split{$cnt++} = [$start .. $end] if $gap >= 2;
$old = $line;
}
############# Write HTML file #############################
#my $header;
open (AA, ">fragments.html") or die "Cannot open file:$!";
print AA <<"EndOfHTML";
Colored Gene Walk
EndOfHTML
#print AA "$header\n";
my $red = '';
my $span = '';
my $brk = qq{
\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, $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, $brk);
}
$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 "$brk";
}
}
print AA <<"EndOfHTML";
EndOfHTML
close (AA);