#!/usr/local/bin/perl

#Title "extraction of sequences"
#saved the sample file in bioinfo.txt
use strict;
use warnings;
use IO::File;

my $handle = new IO::File;
$handle->autoflush(1);
$handle->open("<bioinfo.txt")  or die("$!");

my @input_array;
my @new_array;

@input_array=<$handle>;
@input_array = grep {s/#//g} @input_array;

for (my $i=0; $i<$#input_array; $i++){
        chomp $input_array[$i];
        delete $input_array[$i] if $input_array[$i]=~ /((none)|checked|constraints|predicted)/i; #shedding extras
        next unless $input_array[$i];           #ignoring empty lines.
        push  @new_array, $input_array[$i];     #capturing the elements that I need
             }


for(my $i=0;$i<$#new_array;$i++){
        print "$i-$new_array[$i]\n";         #preparing for further processing
        }