#Data from the text file I am using for search terms. Note these sequence ID names represent a subset of the sequences found in the FASTA file I am searching through. The actual text file is much larger, containing 1000s of terms.
BF01013B2E03.f1  
BF01010B1A11.f1  
BF01028B1E03.f1  
BF01029A2C12.f1  
BF01028B2D11.f1 

#Data from input FASTA file. I am searching through this file using the items from the text file shown above. The actual input FASTA file contains 1000s more items
> BF01013B2E03.f1   735 1   735    ABI
CAATCCAAGAACATTTTGAAGAAAAAATCTCTTAAAAAAAAGAAATCAAAACAAGTGATCAAAAATGAAATGAATGGTCA
> BF01010B1A11.f1   782 1   782    ABI
AACGGACNANNCGGCAACCAGGAGGCCTTCCAAGCTGAACTGGGAGAGTGGATCAAGAAG
> BF01028B2D11.f1   674 1   674    ABI
CCAGCACNNNNTNAGATATTAGCCTAGCCTCTATGTCGTATTTGTATTTCNNCTAGTTTTTCATCCGACTTTTTTGGATC

#output file note the output file has only one sequence in it. This is clearly not what I want. Something is wrong, I just can't put my finger on it. 
> BF01028B2D11.f1   674 1   674    ABI
CCAGCACNNNNTNAGATATTAGCCTAGCCTCTATGTCGTATTTGTATTTCNNCTAGTTTTTCATCCGACTTTTTTGGATC

#perl program
#!/usr/bin/perl
use strict;
use File::Basename;
my $database;
my $data = shift(@ARGV);
my $input_file = shift(@ARGV);
my $infile;
my $match;
my $output_file;
my $ESTs_W_SNPs;
$output_file = "ESTsWsnpsANDgoodCoverage.fasta";
open ($database,'<', $data) or die "Cannot open $data\n";
while ($match = <$database>)
{
     chomp $match;
     open (IN, $input_file) || die "Can't open input file. Please provide a valid input filename.\n";
     open ($ESTs_W_SNPs, '>', $output_file) or die "Cannot write to $output_file\n";
       my ($seq, $prevhead) = (0, "", '');
       while(<IN>)
       {
         my $line = $_;
         $line =~ s/\r\n/\n/; 
         chomp $line;
       	$seq.= uc($line) if(eof(IN));
         if (/\>(.*)/ || eof(IN))
    	 {
         my $head=$1;
         printf $ESTs_W_SNPs ">$prevhead\n$seq\n" if($prevhead =~ /$match/);
         $prevhead = $head;
         $seq='';
	 }
        else
        {
        $seq.=$line;
        }
    }
close (IN);
close ($ESTs_W_SNPs);
}