#!/usr/bin/perl

# ELink (batch) - EFetch

use strict;
use NCBI_PowerScripting;

my (%params, %links);
my @db = qw(protein nucleotide, gene);
my $link;

my $dir ='/home/';
opendir (DIR,$dir)or die $!;

while  (my $file = readdir (DIR)) {
    next unless (-f "$dir/$file");
    next unless ($file =~m/\. gi$/);

my @data;
open (MYFILE,$file) or die "cannot open $file:$!";
open (OUT,">$file.data") or die "cannot open $file:$!";

#ELink

$params{db} = $db[0];
$params{id} = '';

%links = elink_batch_to($db<a href="?node=1">1</a>, %params);

#EFetch

foreach $link (keys %links) {
   
  %params = extract_links($link, %links);
  $params{outfile} = $link . '.dat';
  $params{retmode} = 'text';

  if ($link =~ /nuccore/) {
    $params{rettype} = 'fasta';
  }
  
  efetch_batch(%params);
   print nuccore;

}