my %hash1;
open my $IN, "file1.txt" or die $!;
my $header = <$IN>; ## use if the file has a header otherwise leave it
while(<$IN>){
  chomp $_;
  my @line = split(',',$_); ## split the line to get the sample name and its values
  $hash1{$line[0]} = 1; ## if your first column is a sample name or change it accordingly
}
close($IN);

##</code><code>##

my %CommonSampleNames

open my $IN1, "file2.txt" or die $!;
my $head = <$IN1> ;## again use it if it has a header

while(<$IN1>){
chomp $_;
my @line = split(',', $_);
if(exists $hash1{$line[0]} ){ ## $line[0] is the sample name column
$CommonSampleNames{$line[0]} = 1;
}
}
close($IN1);

##</code><code>##

my %supHash

open my $ref, "ref.txt" or die $!;
$head = <$ref>; ## if header is present
while(<$ref>){
chomp $_;
my @line = split(',', $_);  ## if it is a csv file
if(exists $CommonSampleNames{$line[0]} ){
$supHash{$ine[0]} = $line[1]; ## if second column has reference names
}

}
close($ref);