use Bio::DB::Fasta;


my $db = new Bio::DB::Fasta("Library.fa");

open(INPUT1, "Library.fa") or die "Cannot open Hprot.fa";
open(INPUT2, "Name.fa") or die "Cannot open Hprot.fa";
open(output, ">result.fa"); 

my(@lines1) = <INPUT1>;
my(@lines2) = <INPUT2>;

while $lines1 eq $lines2 && =~ /^Contig*/
[download]

I've never used Bio::DB::Fasta, but having read the man page for it just now, and looking again the OP task description, I think what you want is something like this:

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

my $db = new Bio::DB::Fasta( "Library.fa" )  # this should be the bigg
+er file
    or die "Failed to create Fasta DB object on Library.fa\n";

open( IDLIST, "Name.fa" );  # this is the list of ID strings
while ( <IDLIST> ) {
    my ($id) = (/^>(\S+)/);  # capture the id string (without the init
+ial ">")
    print ">$id\n", $db->seq( $id ), "\n";
}
[download]

As for the code you've just posted, you didn't really try to use the DB::Fasta module, and you don't seem to understand the syntax for a while loop (you need parens around the conditional, and a block of code to be the body of the loop). As for doing a regex match:  /regex/ by itself will test the contents of $_, whereas $var =~ /regex/ tests the contents of $var; what you have,  blahblah && =~ /regex/ is a syntax error.

Also, you need to be aware that "@line1" is a completely different thing (different variable with different storage) from "$line1". To refer to an element of an array, you need square brackets and an array index:  $line1[0] etc.

hello, thanks for the code and comments. I have try to run the code, it creates a ouput file .fa.dir with lots of special characters and I couldnt read it. I dont know whats going wrong. Kindly suggest the solution. thanks!

Hi, thanks for the code. But I have tried to run this, its creates Library.fa.index with lots of special characters unreadable sequences.

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]

Hi Nemo2, I was absent. You already have had some solutions. This is the way I used, using BioPerl.

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

my $database;
my $fasta_library;
my %records;

#  name of the library file - (here it is hardcoded)
$fasta_library = 'Poptr1_FilteredModels_transcripts.fa';

# creates the database of the library, based on the file
$database = Bio::DB::Fasta->new("$fasta_library");

# now, it parses the file with the fasta headers you want to get
while (<STDIN>) {
    chomp (my $seq_id = $_);
    
    my $record = $database->get_Seq_by_id("$seq_id");
    
         # incorporates the header and sequence to the hash
         # key = header ; value = sequence
    $records{$seq_id} = $record->seq();

}

# print all the key-value pairs (
for (sort keys (%records)) {
    print ">$_\n$records{$_}\n";
}

exit;
[download]