Instead of using an array for ids it may be better to use a hash, something like this: 
#! perl --
use strict;
use warnings;


@ARGV == 3 or die "usage: $0 ID-file CSV-file CSV-output\n";

my $forextract = shift;    # IDs to be extracted, 1 per row , further 
+info tab delimited
                        #header[0] is matched against header of dtp_al
+l
my $dtp_all    = shift;    # csv CANCER60xxx.lis....
my $dtp_my     = shift;    # csv output

print "Warning: The file with items to extract has to have a header - 
+the first column name will be matched.\n";
open my $IDS, '<', $forextract or die "Opening $forextract failed: $!"
+;

my ( $myID, %ids );
while ( <$IDS> ) {
    /^\s*([^\t]+?)\s*\t/ or next;
    if ( $. == 1 ) {
        $myID = $1;
        }
    else {
        $ids{ $1 } = 1;
        }
    }

close $IDS;


open my $ALL, '<', $dtp_all or die "Opening $dtp_all failed: $!";
open my $MY,  '>', $dtp_my  or die "Opening $dtp_my failed: $!";

# copy the header
my $header = <$ALL>;
print $MY $header;
my @colnames = split /,/, $header, -1;

my $colN;
for my $col ( 0 .. $#colnames ) {
    if ( $colnames[ $col ] eq $myID ) {
        $colN = $col;
        last;
        }
    }
unless ( defined $colN ) {
    die "Column $myID not found.\n";
    }

# parse the input line by line, when ids matched write the line into t
+he output
while ( my $line = <$ALL> ) {
    my $col = ( split /,/, $line, -1 )[ $colN ];
    s/^\s+//, s/\s+$// for $col;
    if ( exists $ids{ $col } ) {
        print $MY $line;
        }
    }

close $MY or die "Not completed $dtp_my\n";
close $ALL;

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In reply to Re: Uninitialized value in string eq error but I initialized by jwkrahn
in thread Uninitialized value in string eq error but I initialized by karpatov

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