I want to be able to retrieve all refseq fasta sequences for a list of organisms. I am using the code below from the EUtilities cookbook which works for a single organism name.

use Bio::Perl;
use Bio::DB::EUtilities;
use Bio::DB::RefSeq;

# set optional history queue
my $factory = Bio::DB::EUtilities->new(-eutil      => 'esearch',
                                       -email      => 'me@foo.com',
                                       -db         => 'nuccore',
                                       -term       => 'Prevotella[ORGN] AND srcdb_refseq[PROP]',
                                       -usehistory => 'y');

my $count = $factory->get_count;
# get history from queue
my $hist  = $factory->next_History || die 'No history data returned';
print "History returned\n";
# note db carries over from above
$factory->set_parameters(-eutil   => 'efetch',
                         -rettype => 'fasta',
                         -history => $hist);

my $retry = 0;
my ($retmax, $retstart) = (500,0);

open (my $out, '>', 'test_list_seqs.fa') || die "Can't open file:$!";

RETRIEVE_SEQS:
while ($retstart < $count) {
    $factory->set_parameters(-retmax   => $retmax,
                             -retstart => $retstart);
    eval{
        $factory->get_Response(-cb => sub {my ($data) = @_; print $out $data} );
    };
    if ($@) {
        die "Server error: $@.  Try again later" if $retry == 5;
        print STDERR "Server error, redo #$retry\n";
        $retry++ && redo RETRIEVE_SEQS;
    }
    print "Retrieved $retstart";
    $retstart += $retmax;
}
close $out;

` I have attempted to read an organism name list from a file and retrieve sequences that way but that is giving me what I think may be the entire genbank fasta sequences from any database and any organism. Has anyone done a bulk retrieval before? Here is my attempt to get sequences from an organism name file.:

 #!/usr/bin/perl
use strict;
use warnings;
use Bio::Perl;
use Bio::DB::EUtilities;
use Bio::DB::RefSeq;

open(INFILE,"<C:/Users/workspace/general/test_organism_name.txt") or die "Cannot open infile: $!";

while(<INFILE>){
    chomp;
    my $name = $_;
                 my $term = '"$name",[ORGN] AND srcdb_refseq[PROP]';

# set optional history queue
my $factory = Bio::DB::EUtilities->new(-eutil      => 'esearch',
                                       -email      => 'me@foo.com',
                                       -db         => 'nuccore',
                                       -term       =>  '$term',
                                       -usehistory => 'y');

my $count = $factory->get_count;
# get history from queue
my $hist  = $factory->next_History || die 'No history data returned';
print "History returned\n";
# note db carries over from above
$factory->set_parameters(-eutil   => 'efetch',
                         -rettype => 'fasta',
                         -history => $hist);

my $retry = 0;
my ($retmax, $retstart) = (500,0);

open (my $out, '>', 'test_list_seqs.fa') || die "Can't open file:$!";

RETRIEVE_SEQS:
while ($retstart < $count) {
    $factory->set_parameters(-retmax   => $retmax,
                             -retstart => $retstart);
    eval{
        $factory->get_Response(-cb => sub {my ($data) = @_; print $out $data} );
    };
    if ($@) {
        die "Server error: $@.  Try again later" if $retry == 5;
        print STDERR "Server error, redo #$retry\n";
        $retry++ && redo RETRIEVE_SEQS;
    }
    print "Retrieved $retstart";
    $retstart += $retmax;
}
close $out;
}
close INFILE;

Thanks!