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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: DB.t,v 1.29 2002/01/19 22:26:17 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS);
my $error;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
$error = 0;
if( $@ ) {
use lib 't';
}
use Test;
$NUMTESTS =51;
plan tests => $NUMTESTS;
eval { require IO::String };
if( $@ ) {
print STDERR "IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests.\n";
for( 1..$NUMTESTS ) {
skip("IO::String not installed",1);
}
$error = 1;
}
}
if( $error == 1 ) {
exit(0);
}
require Bio::DB::GenBank;
require Bio::DB::GenPept;
require Bio::DB::SwissProt;
my $testnum;
my $verbose = 0;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my ($gb,$seq,$seqio);
# get a single seq
eval {
ok defined ( $gb = new Bio::DB::GenBank('-verbose'=>$verbose) );
ok( defined ($seq = $gb->get_Seq_by_id('MUSIGHBA1')));
ok( $seq->length, 408);
ok( defined ($seq = $gb->get_Seq_by_acc('AF303112')));
ok($seq->length, 1611);
ok( defined ($seq = $gb->get_Seq_by_version('AF303112.1')));
ok($seq->length, 1611);
ok( defined ($seq = $gb->get_Seq_by_gi('405830')));
ok($seq->length, 1743);
};
if ($@) {
warn "Warning: Couldn't connect to Genbank with Bio::DB::GenBank.pm!\nError: $@\nDo you have network access? Skipping all other tests";
foreach ( $Test::ntest..$NUMTESTS ) { skip('no network access',1); }
exit(0);
}
$seq = $seqio = undef;
eval {
ok( defined($seqio = $gb->get_Stream_by_batch([ qw(J00522 AF303112
2981014)])));
ok($seqio->next_seq->length, 408);
ok($seqio->next_seq->length, 1611);
ok($seqio->next_seq->length, 1156);
};
if ($@) {
warn "Batch access test failed.\nError: $@\n";
foreach ( $Test::ntest..$NUMTESTS ) { skip('no network access',1); }
exit(0);
}
$seq = $seqio = undef;
eval {
ok defined($gb = new Bio::DB::GenPept('-verbose'=>$verbose));
ok( defined($seq = $gb->get_Seq_by_id('195055')));
ok( $seq->length, 136);
$seq = $gb->get_Seq_by_acc('AAC06201');
ok(defined $seq);
ok($seq->length, 353);
$seqio = $gb->get_Stream_by_batch([ qw(AAC06201 195055)]);
ok( defined $seqio);
ok( $seqio->next_seq->length(), 353);
ok( $seqio->next_seq->length(), 136);
};
if ($@) {
warn "Warning: Couldn't connect to Genbank with Bio::DB::GenPept.pm!\n$@";
foreach( $Test::ntest..$NUMTESTS ) {
skip('could not connect with GenPept',1);
}
exit(0);
}
$seq = $seqio = undef;
eval {
ok defined($gb = new Bio::DB::SwissProt('-verbose'=>$verbose));
ok(defined($seq = $gb->get_Seq_by_id('YNB3_YEAST')));
ok( $seq->length, 125);
ok($seq->division, 'YEAST');
ok(defined($seq = $gb->get_Seq_by_acc('P43780')));
ok( $seq->length, 103);
ok( defined( $seq = $gb->get_Seq_by_acc('O39869')));
ok( $seq->length, 56);
ok($seq->primary_id, 'O39869');
ok($seq->division, 'UNK');
# test for bug #958
$seq = $gb->get_Seq_by_id('P18584');
ok( defined $seq );
ok( $seq->length, 497);
ok( $seq->primary_id, 'DEGP');
ok( $seq->display_id, 'DEGP_CHLTR');
ok( $seq->division, 'CHLTR');
ok( defined($gb = new Bio::DB::SwissProt('-verbose'=>$verbose,
'-retrievaltype' => 'tempfile')));
ok(defined($seqio = $gb->get_Stream_by_id(['KPY1_ECOLI', 'KPY1_HUMAN'])));
undef $gb; # testing to see if we can remove gb
ok( defined($seq = $seqio->next_seq()));
ok( $seq->length, 470);
ok( defined($seq = $seqio->next_seq()));
ok( $seq->length, 530);
};
if ($@) {
print STDERR "Warning: Couldn't connect to SwissProt with Bio::DB::Swiss.pm!\n$@";
foreach ( $Test::ntest..$NUMTESTS) {
skip('could not connect to swissprot',1);
}
exit(0);
}
$seq = undef;
# test the temporary file creation and fasta
eval {
ok defined ( $gb = new Bio::DB::GenBank('-verbose' =>$verbose,
'-format' => 'fasta',
'-retrievaltype' => 'tempfile') );
ok( defined ($seq = $gb->get_Seq_by_id('MUSIGHBA1')));
ok($seq->length, 408);
$seq = $gb->get_Seq_by_acc('AF303112');
ok( defined $seq);
ok( $seq->length, 1611);
# batch mode requires genbank format
$gb->request_format("genbank");
ok(defined($seqio = $gb->get_Stream_by_batch([ qw(J00522 AF303112
2981014)])));
ok( $seqio->next_seq->length, 408);
undef $gb; # test the case where the db is gone,
# but a temp file should remain until seqio goes away.
ok($seqio->next_seq->length, 1611);
ok($seqio->next_seq->length, 1156);
};
if ($@) {
warn "Warning: Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm!\n $@\n";
foreach ( $Test::ntest..$NUMTESTS ) {
skip('could not connect to Genbank',1);
}
}
$seq = $seqio = undef;
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