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# -*-Perl-*- Test Harness script for Bioperl
# $Id: EMBL.t 16091 2009-09-15 22:11:15Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 16,
-requires_modules => [qw(IO::String HTTP::Request::Common)],
-requires_networking => 1);
use_ok('Bio::DB::EMBL');
}
my $verbose = test_debug();
my ($db,$seq,$seqio);
# get a single seq
$seq = $seqio = undef;
SKIP: {
ok defined($db = Bio::DB::EMBL->new(-verbose=>$verbose));
ok(defined($seq = $db->get_Seq_by_acc('J00522')));
is( $seq->length, 408);
ok defined ($db->request_format('fasta'));
eval {ok(defined($seq = $db->get_Seq_by_acc('J02231')))};
skip('could not connect to embl',2) if $@;
is( $seq->id, 'embl|J02231|J02231');
is( $seq->length, 200);
ok( defined($db = Bio::DB::EMBL->new(-verbose=>$verbose,
-retrievaltype => 'tempfile')));
eval {ok(defined($seqio = $db->get_Stream_by_id(['BUM'])))};
skip('could not connect to embl',2) if $@;
undef $db; # testing to see if we can remove gb
ok( defined($seq = $seqio->next_seq()));
cmp_ok( $seq->length, '>=', 1);
}
$seq = $seqio = undef;
SKIP: {
$db = Bio::DB::EMBL->new(-verbose => $verbose,
-retrievaltype => 'tempfile',
-format => 'fasta'
);
eval{ok( defined($seqio = $db->get_Stream_by_acc(['J00522 AF303112 J02231'])))};
skip('could not connect to embl',3) if $@;
my %seqs;
# don't assume anything about the order of the sequences
while ( my $s = $seqio->next_seq ) {
my ($type,$x,$name) = split(/\|/,$s->display_id);
$seqs{$x} = $s->length;
}
is($seqs{'J00522'},408);
is($seqs{'AF303112'},1611);
is($seqs{'J02231'},200);
}
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