I have been stuck with some script!

Well I made this script in 2008 and now I am using with some modifications and I get error!

#!/usr/bin/perl -w

use strict;
use Data::Dumper;

sub getSequences ($) {

    my $file = $_[0];
    open (INFILE, "<$file") || die "Error1 in opening in file: $file. $!\n";

        my @lines = <INFILE>;
        my $header; my %header2seq = ();

        foreach my $line (@lines) {
            chomp $line;
            if ($line =~ /^(>.+)$/o) {
                $header = $1;
            }
            else {$header2seq {$header} .= $line; }
        }
#print %header2seq;
    close (INFILE);
    return (\%header2seq);
}

sub MakeSpList ($) {

    my $sp_list = $_[0]; my %sp_names = ();
    open (INFILE2, "<$sp_list") || die "Error2 in opening in file: $sp_list. $!\n";
    my @sps = <INFILE2>;
    foreach my $line (@sps) { chomp $line; $sp_names {$line} = 1; }
    close (INFILE2);
#print Dumper (%sp_names);
    return (\%sp_names);
}

sub CompareSpList2Sequences ($$$) {
     my $ref_header2seq = $_[0] ; my $ref_sp_names = $_[1]; my $file = $_[2];
     open (OUTFILE, ">$file.subdata") || die ("Error3 in opening out file: $file.subdata. $!\n");
     foreach my $key (keys %$ref_header2seq) {
         $key =~ m/^>([A-Z]+[0-9]+[A-Z+]).+$/o;
        #print "$1\n";
          my $header_sub = $1;
         #print $header_sub, "\n";
         #print $ref_sp_names, "\n";
         if (exists $ref_sp_names -> {$header_sub}) {
             my $seq = $ref_header2seq -> {$key};
             print OUTFILE ">$key\n$seq\n";
         }
     }    
     close (OUTFILE);
     return "42";
}

my $fasta_seqs = $ARGV[0]; my $sp_list = $ARGV[1];

my $ref_header2seq = getSequences ($fasta_seqs);
my $ref_sp_names = MakeSpList ($sp_list);
CompareSpList2Sequences ($ref_header2seq , $ref_sp_names, $fasta_seqs);

exit;

What I want to do is:

I have a fasta file with sequences:

>YAL004W YAL004W SGDID:S000002136, Chr I from 140760-141407, Genome Release 64-2-1, Dubious ORF, "Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; completely overlaps verified gene SSA1/YAL005C" ATGGGTGTCACCAGCGGTGGCCTTAACTTCAAAGATACCGTCTTCAATGGACAACAAAGAGACATCGAAAGTACCACCACCCAAGTCGAAAATCAAGACGTGTTCTTCCTTACCCTTCTTGTCCAAACCGTAAGCAATGGCAGCGGCGGTAGGTTCGTTAATAATACGCAAGACATTCAAACCAGCAATGGTACCAGCATCCTTGGTAGCTTGTCTTTGAGAATCGTTGAA
>YAL005C SSA1 SGDID:S000000004, Chr I from 141431-139503, Genome Release 64-2-1, reverse complement, Verified ORF, "ATPase involved in protein folding and NLS-directed nuclear transport; member of HSP70 family; forms chaperone complex with Ydj1p; localized to nucleus, cytoplasm, and cell wall; 98% identical with paralog Ssa2p, but subtle differences between the two proteins provide functional specificity with respect to propagation of yeast [URE3] prions and vacuolar-mediated degradations of gluconeogenesis enzymes; general targeting factor of Hsp104p to prion fibrils" ATGTCAAAAGCTGTCGGTATTGATTTAGGTACAACATACTCGTGTGTTGCTCACTTTGCTAATGATCGTGTGGACATTATTGCCAACGATCAAGGTAACAGAACCACTCCATCTTTTGTCGCTTTCACTGACACTGAAAGATTGATTGGTGATGCTGCTAAGAATCAAGCTGCTATGAATCCTTCGAATACCGTTTTCGACGCTAAGCGTTTGATCGGTAGAAACTTCAAC

and I have another file with ID's:

>YAL005C
>YAL012W

I want to retrieve the sequences and the all header when match with ID's file but I get error: don't print nothing!

Please can you help me?

Thanks in advance

• I already searched for other methods (and I can't get the results either) but I really want to know about this error!
• no bioperl please!