just install bioperl and use the module Bio::SeqIO to read in this FASTA format ... like this. Note that I haven't tested it.. but it should work in this fashion.

use strict; # you do use strict don't you?
use Bio::SeqIO;
# your file containing the patterns
open (INP,"data.txt") || die "cant find it!"; 

while (my $line = <INP>) {
  chomp $line;
  # separate pattern from filename
  my ($filename,$pattern) = split (/\s+/,$line);

  #open the file that should be searched
  my $seqio_object = Bio::SeqIO->new(-file => $filename, -format=>"fas
+ta");

  #loop through all the fasta sequences
  while ($seq_object = $seqio_object->next_seq){
     my $sequence = $seq_object->seq;
     my $id = $seq_object->display_id;     
    #check if pattern exists
    if ($sequence =~ /$pattern/g) {
       print "$pattern found in $id in file $filename\n";
     }
  }

}
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However, on another note, its probably better to post Bioperl questions on the bioperl mailing list. Google for it.