help needed to retrieve fasta reads from fasta db

[prashanthpnu]

Hi There,

I am quite new to Linux and Bioperl. I have used blast to find alignments. I need to store the complete query sequence of all hit reads to a seperate file (not just hit sequence). I tried regular expressions..may be i am not using the right match string..I also tried fastacmd command..

So far no luck in extracting few reads from fasta file.

Please help me!

Thanks in advance..

-Prashanth

[prashanthpnu]

found this

Found code here to retrieve fasta for specific accessions: http://biostar.stackexchange.com/que...3gb-fasta-file

use strict;
use Bio:B::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
$database = Bio:B::Fasta->new("$fasta_library") or die "Failed to creat 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 initial ">")
my $header = $database->header($id);
#print "$header\n";
print ">$header\n", $database->seq( $id ), "\n";
print OUTPUT ">$header\n", $database->seq( $id ), "\n";
}

exit;