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# -*-Perl-*- Test Harness script for Bioperl
# $Id: BioFetch.t 16091 2009-09-15 22:11:15Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 36,
-requires_modules => [qw(IO::String LWP::UserAgent)],
-requires_networking => 1);
use_ok('Bio::DB::BioFetch');
}
my $verbose = test_debug();
my $dbwarn = "Warning: Couldn't connect to EMBL with Bio::DB::BioFetch!\n";
my ($db,$db2,$seq,$seqio);
SKIP :{
# get a single seq
ok defined($db = Bio::DB::BioFetch->new(-verbose => $verbose));
# get a RefSeq entry
ok $db->db('refseq');
eval {
$seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq VERSION
};
skip($dbwarn, 4) if $@;
isa_ok($seq, 'Bio::SeqI');
is($seq->accession_number,'NM_006732');
is($seq->accession_number,'NM_006732');
is( $seq->length, 3776);
}
SKIP: {
# EMBL
$db->db('embl');
eval {
$seq = $db->get_Seq_by_acc('J02231');
};
skip($dbwarn, 3) if $@;
isa_ok($seq, 'Bio::SeqI');
is($seq->id, 'J02231');
is($seq->length, 200);
}
SKIP: {
eval {
$seqio = $db->get_Stream_by_id(['BUM']);
};
skip($dbwarn, 3) if $@;
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);
}
SKIP: {
#swissprot
ok $db2 = Bio::DB::BioFetch->new(-db => 'swissprot');
eval {
$seq = $db2->get_Seq_by_id('YNB3_YEAST');
};
skip($dbwarn, 5) if $@;
isa_ok($seq, 'Bio::SeqI');
is($seq->length, 125);
is($seq->division, 'YEAST');
$db2->request_format('fasta');
eval {
$seq = $db2->get_Seq_by_acc('P43780');
};
skip($dbwarn, 2) if $@;
isa_ok($seq, 'Bio::SeqI');
is($seq->length,103);
}
$seq = $seqio = undef;
SKIP: {
ok $db = Bio::DB::BioFetch->new(-retrievaltype => 'tempfile',
-format => 'fasta',
-verbose => $verbose
);
$db->db('embl');
eval {
$seqio = $db->get_Stream_by_id('J00522 AF303112 J02231');
};
skip($dbwarn, 7) if $@;
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);
}
SKIP: {
ok $db = Bio::DB::BioFetch->new(-db => 'embl', -verbose => $verbose ? $verbose : -1);
# check contig warning (WebDBSeqI)
eval {
$seq = $db->get_Seq_by_acc('NT_006732');
};
like($@, qr{contigs are whole chromosome files}, 'contig warning');
eval {
$seq = $db->get_Seq_by_acc('NM_006732');
};
skip($dbwarn, 3) if $@;
isa_ok($seq, 'Bio::SeqI');
is($seq->length,3776);
}
# unisave
SKIP: {
ok $db = Bio::DB::BioFetch->new(-db => 'unisave',
-verbose => $verbose);
eval {
$seq = $db->get_Seq_by_acc('LAM1_MOUSE');
};
skip($dbwarn, 3) if $@;
isa_ok($seq, 'Bio::SeqI');
is($seq->display_id, 'LAM1_MOUSE');
is($seq->accession, 'P14733');
is($seq->length, 587);
}
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