use strict;
use warnings;

## Variables
my %sampleID;
my %sampleValue;


## Opening first file
open my $IN, "sample.txt" or die $!;
my $header = <$IN>;

while(<$IN>){
	chomp $_;
	my @line = split('\t', $_);
	$sampleID{$line[0]} = 1; ## Sample ID and Pam50 prediction
}
close($IN);
print "Total number of sample ID: ", scalar(keys %sampleID),"\n"; ## 1000 columns

## Sample Value Data
open $IN, "sampleValue.txt" or die $!;

## Columns are sample names from file1
$header = <$IN>;
my @samples = split("\t", $header); ## 
print "Total samples: ",scalar(@samples),"\n"; ## 1500

## loop for all the samples ids or the columns I am interested in
for(my $i = 1; $i <= $#samples; $i++){ ## bcos the first instance is called header of the column 1
	my $sample = $samples[$i];
	$sampleValue{$sample} = $i if (exists $sampleID{$sample});
}

my $col = "";  
foreach my $key (keys %sampleValue){
	$col = $sampleValue{$key}.",".$col;
}
chop($col);
print $col,"\n"; ## string of all the columns I am interested in

## The reason I do the above loop because I don't want to look for the interested ## cols thru the hash for every line of the file

## Reading the sample Value file
while(<$IN>){
	chomp $_;
	print $_,"\n";
	my @line = split("\t", $_);
	@line = @line[ split /,/, $col]; ## previously it was @line = @line[$col] -- and i was getting error because $col is a string
	print @line,"\n";
}