What is result if File A score is 50 and File B score is 40 ?. Assuming that anything that isn't NC or PASS is FAIL then your code can be reduced to something like this. 
#!perl
use strict;

open (PASS, ">pass.rpt") || die "ERROR: cannot open";
open (FAIL, ">fail.rpt") || die "ERROR: cannot open";
open (NC, ">noCheck.rpt") || die "ERROR: cannot open";

# for test
my @PASS=();
my @FAIL=();
my @NC=();
my ($ncc,$pc,$fc);

# test data if required
my @arr1=();# = ('A;-50','B;51','C;51','D;55');
my @arr2=();# = ('A;51' ,'B;39','C;41','F;57');

file_ext('fileA.txt',\@arr1);
file_ext('fileB.txt',\@arr2);
check();

print "\nTotal PASS match: $pc\n\n";
print "$_\n" for @PASS;
print "\nTotal FAIL match: $fc\n\n";
print "$_\n" for @FAIL;
print "\nTotal NC match: $ncc\n\n";
print "$_\n" for @NC;


sub file_ext {
  my ($file,$ar) = @_;
  open (FILE,'<',$file) or die "Could not open $file";
  while (<FILE>){
    chomp;
    # name = first field, score = last field
    my @f = split /\s+/;
    #print "$f[0] $f[-1]\n";
    push @$ar,"$f[0];$f[-1]";
  }
}


sub check {
  foreach my $data1 (@arr1) { 
    my ($ep1,$s1) = split ';',$data1;

    foreach my $data2 (@arr2) {
      my ($ep2,$s2) = split ';',$data2;
      
      next if ($ep1 ne $ep2);  
      
      # negatives in fileA score
      if ($s1 =~ /-/){  
        $ncc++;
        my $line = sprintf "%-20s %4d %4d",$ep1,$s1,$s2;
        print NC $line."\n";
        push @NC,$line;
      }
      
      # pass
      elsif (($s1 > 50) && ($s2 >40)){
        $pc++;
        my $line = sprintf "%-20s %4d %4d",$ep1,$s1,$s2;
        print PASS $line."\n";
        push @PASS,$line;
      }
      
      #fail
      else {
        $fc++;
        my $line = sprintf "%-20s %4d %4d",$ep1,$s1,$s2;
        print FAIL $line."\n";
        push @FAIL,$line;
      }
    }    
  }
}

=head1 fileA.txt
Jane_let [0] (sa) 58.78 r 66.15 0.00 -33
Alfert_pipe (sa) 74.72 r 92.72 0.00 82
Olive_pipe[8] (sa) 64.28 f 25.40 0.00 58
mass/excel/i60 86.21 r 59.90 0.00 68
Anne_let (sa) 51.98 f 12.69 0.00 -39
yuki/099/pipe 76.52 r 94.32 0.00 -82
frey/let/sa/y589 47.79 f 99.00 0.00 78
alan/excel/sa/y589 97.00 f 96.00 0.00 -70 

=head1 fileB.txt
Ash_let[9] (sa) 58.78 r 66.15 0.00 33
Alfert_pipe (sa) 74.72 r 92.72 0.00 57
Olive_pipe[8] (sa) 64.28 f 25.40 0.00 20
mass/excel/i60 86.21 r 59.90 0.00 16
Sam_let (sa) 51.98 f 12.69 0.00 -39
yuki/099/pipe 76.52 r 94.32 0.00 82
frey/let/sa/y589 47.79 f 99.00 0.00 30
alan/excel/sa/y589 67.00 f 96.00 0.00 -90 
=cut

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If the run time is too slow then consider a hash based solution rather than using arrays.
poj

In reply to Re: Perl: How to perfectly match specific data between two files and do comparison? by poj
in thread Perl: How to perfectly match specific data between two files and do comparison? by WWq

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