The sequence file could be as large as 40Mb and the list could contain as many as 35000 sequences. I'm new to perl and have been struggling with this for a couple of days. Here's the part I wrote, but it doesn't give me the full list I want:( 
my $nohit_list = "data.txt";
open (NOHIT, "<$nohit_list")or die "can't open file: $!";
foreach $line (<NOHIT>) {
    print $line;
my $all = "all.txt";
open (ALL, "<$all") or die "can't open file: $!";
{    local $/ = '>';
    @fasta = <ALL>;
}
my $requery = "requery.txt";
open (FASTA, ">$requery")or die "can't open file: $!";
 my @nohit_fasta = ();
 @nohit_fasta = grep /$line/,@fasta;
 print FASTA @nohit_fasta;

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In reply to Re^2: compare a list from one file with another text file by sm2004
in thread compare a list from one file with another text file by sm2004

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