I changed the code in a way that prints the entire header. The thing that happens is that, if your id is long and you need to have the entire information by printing $id you may lose the informative part from any space onward. 

 #!/usr/bin/perl

use strict;
use Bio::DB::Fasta;

my $database;
my $fasta_library;
my %records;
open IDFILE, "NBS_LRR_IDs.txt" or die $!;
open OUTPUT, ">NC_003070_NBS-LRR.faa" or die $!;
#  name of the library file - (here it is hardcoded)
$fasta_library = 'NC_003070_all_chr.faa';

# creates the database of the library, based on the file
$database = Bio::DB::Fasta->new("$fasta_library") or die "Failed to cr
+eate Fasta DP object on fasta library\n";


# now, it parses the file with the fasta headers you want to get
while (<IDFILE>) {



      my ($id) = (/^>*(\S+)/);  # capture the id string (without the i
+nitial ">")
      my $header = $database->header($id);
      #print "$header\n";
      print ">$header\n", $database->seq( $id ), "\n";
      print OUTPUT  ">$header\n", $database->seq( $id ), "\n";
}

exit;

[download]

In reply to Re^4: comparing two fasta files by sesemin
in thread comparing two fasta files by nemo2

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