Batch download GENBANK entries via TogoWS.

genbankn_batch_downloader.pl

#!/usr/bin/env perl
use strict;
use warnings;

my $base = "togows.dbcls.jp/entry/nucleotide";

my ($prefix, $from_id, $to_id) = (@ARGV);

if($from_id > $to_id) {
    ($from_id, $to_id) = ($to_id, $from_id);
}

my $seq = "";
foreach my $id (map{$prefix.$_}($from_id..$to_id)) {
    my $url = sprintf("http://$base/$id");
    print "$id\n";
    $seq .= `curl -L $url`;
    sleep(1);
}

open my $fh, ">", sprintf("%s_%d-%d.fasta", $prefix, $from_id, $to_id);
print $fh $seq;
close $fh;