#!/usr/bin/perl -w -s
##########INPUT Sequence, concatenated into a single string##########
#example of chomp . 
#
unless(@ARGV==1) {die "please provide name of the file in the command line!!\n";}
my$filename=$ARGV[0]; #takes filenname from input line
my $outfile="chomp_example";
open(OUT, "> $outfile") or die "cannot open $outfile:$!"; #assigns filehandle IN to filename or dies

my$seq=''; #assigns empty string
my$line='';
MAIN: 
{open(IN, "< $filename") or die "cannot open $filename:$!"; #assigns filehandle IN to filename or dies
while(defined($line=<IN>)){

	chomp($line);
	$seq .= $line ;
	}
close (IN);		
print "with chomp:\n$seq\n\n\n"; 
print OUT "with chomp:\n$seq\n\n\n"; 


$seq=''; #assigns empty string
$line='';
open(IN, "< $filename") or die "cannot open $filename:$!";
while( defined($line=<IN>)){
		$seq .= $line ;
		}
close (IN);		
print "without chomp:\n$seq\n\n\n"; 
print OUT "without chomp:\n$seq\n\n\n"; 

$seq=''; #assigns empty string
$line='';
open(IN, "< $filename") or die "cannot open $filename:$!";
while( defined($line=<IN>)){
                $seq .= chomp($line);
	       	}
close (IN);
print "with chomp inadvertantly used as function:\n$seq\n\n\n";
print OUT "with chomp inadvertantly used as function:\n$seq\n\n\n";					

$seq=''; #assigns empty string
$line='';
open(IN, "< $filename") or die "cannot open $filename:$!";
my@input=<IN>;

close (IN);
print "without chomp using array:\n@input\n\n\n";
print OUT  "without chomp using array:\n@input\n\n\n";


$seq=''; #assigns empty string
$line='';
@input=();
open(IN, "< $filename") or die "cannot open $filename:$!";
@input=<IN>;
foreach (@input) {chomp$_};
close (IN);
print "with chomp using array:\n@input\n\n\n";
print OUT "with chomp using array:\n@input\n\n\n";


$seq=''; #assigns empty string
$line='';
@input=();
open(IN, "< $filename") or die "cannot open $filename:$!";
@input=<IN>;
foreach $line (@input) {
	$line =chomp$line;}
close (IN);
print "with chomp-erroniously used using array:\n@input\n\n\n";
print OUT "with chomp-erroniously used using array:\n@input\n\n\n";

$seq=''; #assigns empty string 
$line='';
@input=();
open(IN, "< $filename") or die "cannot open $filename:$!";
@input=<IN>;
foreach (@input) {chomp$_};
close (IN);
my $out = join ("",@input);
print "with chomp using array\nand join:\n$out\n\n\n";
print OUT "with chomp using array\nand join:\n$out\n\n\n";


$seq=''; #assigns empty string
$line='';
@input=();
open(IN, "< $filename") or die "cannot open $filename:$!";
@input=<IN>;
foreach (@input) {chomp$_};
close (IN);
$out = join ("\n",@input);
print "with chomp using array\nand join with \\n:\n$out\n\n\n";
print OUT "with chomp using array\nand join with \\n:\n$out\n\n\n";

close (OUT);

					



}