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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
use Test::More;
use Test::RequiresInternet;
use Test::Warn;
use Test::Exception;
use Bio::DB::BioFetch;
my ($db,$db2,$seq,$seqio);
ok defined($db = Bio::DB::BioFetch->new());
{
# get a single seq
# get a RefSeq entry
ok $db->db('refseqn');
$seq = $db->get_Seq_by_acc('NM_006732.2'); # RefSeq VERSION
isa_ok($seq, 'Bio::SeqI');
is($seq->accession_number,'NM_006732');
is($seq->accession_number,'NM_006732');
is( $seq->length, 3776);
}
{
# EMBL
$db->db('embl');
$seq = $db->get_Seq_by_acc('J02231');
isa_ok($seq, 'Bio::SeqI');
is($seq->id, 'J02231');
is($seq->length, 200);
}
{
$seqio = $db->get_Stream_by_id(['AEE33958']);
undef $db; # testing to see if we can remove gb
$seq = $seqio->next_seq();
isa_ok($seqio, 'Bio::SeqIO');
isa_ok($seq, 'Bio::SeqI');
cmp_ok( $seq->length, '>=', 1);
}
ok $db2 = Bio::DB::BioFetch->new(-db => 'swissprot');
SKIP: {
eval { require Data::Stag };
skip "Data::Stag not installed", 5 if $@;
$seq = $db2->get_Seq_by_id('YNB3_YEAST');
isa_ok($seq, 'Bio::SeqI');
is($seq->length, 125);
is($seq->division, 'YEAST');
$db2->request_format('fasta');
$seq = $db2->get_Seq_by_acc('P43780');
isa_ok($seq, 'Bio::SeqI');
is($seq->length,103);
}
$seq = $seqio = undef;
{
ok $db = Bio::DB::BioFetch->new(-retrievaltype => 'tempfile',
-format => 'fasta',
);
$db->db('embl');
$seqio = $db->get_Stream_by_id('J00522 AF303112 J02231');
my %seqs;
# don't assume anything about the order of the sequences
while ( my $s = $seqio->next_seq ) {
isa_ok($s, 'Bio::SeqI');
my ($type,$x,$name) = split(/\|/,$s->display_id);
$seqs{$x} = $s->length;
}
isa_ok($seqio, 'Bio::SeqIO');
is($seqs{'J00522'},408);
is($seqs{'AF303112'},1611);
is($seqs{'J02231'},200);
}
{
ok $db = Bio::DB::BioFetch->new(-db => 'embl');
# check contig warning (WebDBSeqI)
throws_ok (sub { $seq = $db->get_Seq_by_acc('NT_006732') },
qr/contigs are whole chromosome files/,
'contig warning');
warning_like (sub { $seq = $db->get_Seq_by_acc('NM_006732.2') },
qr/RefSeq \(nucleotide\) entry\. Redirecting the request\./,
'Warn redirection from EMBL to RefSeq');
isa_ok($seq, 'Bio::SeqI');
is($seq->length,3776);
}
# unisave
{
ok $db = Bio::DB::BioFetch->new(-db => 'unisave');
$seq = $db->get_Seq_by_acc('P14733');
isa_ok($seq, 'Bio::SeqI');
is($seq->display_id, 'LMNB1_MOUSE');
is($seq->accession, 'P14733');
is($seq->length, 588);
}
done_testing;
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