Hi there, give this a try and let me know how if you have questions.

#!/usr/local/bin/perl
use 5.016; #version >=5.12 turns on strictures by default
use warnings;
use autodie qw/ open close /; #saves typing die all the time


die "Usage: $0 infile1 infile2\n" unless @ARGV == 2;


my %count_cols;
my @cols;
while( <> ) {   # perl will read/process one file in whole then move o
+n to the next
    chomp;
 # get 1st col from each line using an array slice
    push @cols, ( split( /\t/, $_ ) )[0];
}

for ( @cols ) {
    $count_cols{ $_ }++; # hash value = how many times does col name a
+ppear
}

my @intersects; # store columns that appear in both files
for ( keys %count_cols ) {
    if( $count_cols{ $_ } == 2 ) {
        push @intersects, $_; 
    }
}

# open fileA again and extract fields in second column
open IN, "<", "fileA";
while( my $line = <IN> ) {
    chomp $line;
    next if ! $line;
    for my $intersect ( @intersects ) {
        if( $intersect eq ( split( /\t/, $line ) )[0] ) {
            my $result = ( split( /\t/, $line ) )[1];
            say $result; # prints with \n, supported in >5.10
        }
    }
}
close IN;
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