#!/usr/bin/perl
use strict;
use warnings;
use LWP::Simple;
use Data::Dumper;
my $sequence="GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACCAGCCGCGCTTCTGTCCGCCTGCAGGGCATT";
############ 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 $!;
print AA "\n";
print AA "\n";
print AA "\n";
print AA " Colored Gene Walk \n";
print AA "\n";
print AA "\n";
print AA "\n";
print AA "\n";
#print AA "$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, "");
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,"
");
}
$FLAG=1; $pos++;
}
push (@temp, "");
}
}
if($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 "
";
}
}
print AA "\n";
print AA "\n";
print AA "\n";
print AA "\n";
print AA "\n";
close (AA);