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# -*-Perl-*- Test Harness script for Bioperl
# $Id: RefSeq.t 15291 2009-01-05 04:22:36Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 16,
-requires_modules => [qw(IO::String
LWP::UserAgent
HTTP::Request::Common)]);
use_ok('Bio::DB::RefSeq');
use_ok('Bio::DB::GenBank');
use_ok('Bio::DB::EMBL');
}
my $verbose = test_debug() || -1;
my ($db,$seq,$db2,$seq2,$seqio);
# get a single seq
$seq = $seqio = undef;
#test redirection from GenBank and EMBL
#GenBank
ok $db = Bio::DB::GenBank->new('-verbose'=> $verbose, -redirect_refseq => 1);
#EMBL
ok $db2 = Bio::DB::EMBL->new('-verbose'=> $verbose, -redirect_refseq => 1);
eval {
$seq = $db->get_Seq_by_acc('NT_006732');
$seq2 = $db2->get_Seq_by_acc('NT_006732');
};
ok $@;
SKIP: {
test_skip(-tests => 10, -requires_networking => 1);
eval {
ok($seq = $db->get_Seq_by_acc('NM_006732'));
is($seq->length, 3776);
ok $seq2 = $db2->get_Seq_by_acc('NM_006732');
is($seq2->length, 3776);
};
skip "Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!", 10 if $@;
eval {
ok defined($db = Bio::DB::RefSeq->new(-verbose=>$verbose));
ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
is( $seq->length, 3776);
ok defined ($db->request_format('fasta'));
ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
is( $seq->length, 3776);
};
skip "Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!", 6 if $@;
}
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