#!/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);
####
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