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# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqHound.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 15,
-requires_modules => [qw(IO::String LWP::UserAgent)],
-requires_networking => 1);
use_ok('Bio::DB::SeqHound');
}
END {
unlink $Bio::DB::SeqHound::LOGFILENAME if -f $Bio::DB::SeqHound::LOGFILENAME;
}
my $verbose = test_debug();
my ($db,$seq,$seqio);
# get a single seq
$seq = $seqio = undef;
SKIP: {
$db = Bio::DB::SeqHound->new(-verbose=>$verbose);
eval {ok(defined($seq = $db->get_Seq_by_acc('J00522')));};
skip('Could not connect to seqhound, skipping tests', 10) if $@;
is( $seq->length, 408);
ok defined ($db->request_format('fasta'));
eval {ok(defined($seq = $db->get_Seq_by_acc('NP_862707')));};
skip('Could not connect to seqhound, skipping tests', 7) if $@;
is( $seq->accession, 'NP_862707');
is( $seq->length, 227);
ok( defined($db = Bio::DB::SeqHound->new(-verbose=>$verbose,
-retrievaltype => 'tempfile')));
eval {ok(defined($seqio = $db->get_Stream_by_id(['BTACHRE'])));};
skip('Could not connect to seqhound, skipping tests', 3) if $@;
undef $db; # testing to see if we can remove db
ok( defined($seq = $seqio->next_seq()));
is( $seq->length, 1621);
}
$seq = $seqio = undef;
SKIP: {
$db = Bio::DB::SeqHound->new(-verbose => $verbose,
-retrievaltype => 'tempfile',
-format => 'genbank'
);
eval {ok( defined($seqio = $db->get_Stream_by_acc(['J00522', 'AF303112', 'J02231'])));};
skip('Could not connect to seqhound for batch test, skipping tests', 4) if $@;
is($seqio->next_seq->length, 408);
is($seqio->next_seq->length, 1611);
is($seqio->next_seq->length, 200);
}
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