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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: BioFetch_DB.t,v 1.9 2003/10/25 14:52:22 heikki 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 $DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
use lib '.','./blib/lib';
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 = 27;
plan tests => $NUMTESTS;
unless( eval "require IO::String; 1;" ) {
# warn $@;
for( $Test::ntest..$NUMTESTS ) {
skip("IO::String not installed. This means that Bio::DB::BioFetch module is not usable. Skipping tests.",1);
}
$error = 1;
}
}
END {
foreach ( $Test::ntest..$NUMTESTS) {
skip('unable to run all of the Biblio/Biofetch tests - probably no network',1);
}
}
if( $error == 1 ) {
exit(0);
}
require Bio::DB::BioFetch;
my $verbose = -1;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my ($db,$db2,$seq,$seqio);
# get a single seq
$seq = $seqio = undef;
ok defined($db = new Bio::DB::BioFetch(-verbose => $verbose));
eval {
# get a RefSeq entry
ok $db->db('refseq');
$seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq VERSION
$seq ? ok 1 : exit;
ok $seq->accession_number;
# EMBL
$db->db('embl');
ok(defined($seq = $db->get_Seq_by_acc('J00522')));
ok( $seq->length, 408);
ok(defined($seq = $db->get_Seq_by_acc('J02231')));
ok $seq->id, 'BUM';
ok( $seq->length, 200);
ok(defined($seqio = $db->get_Stream_by_id(['BUM'])));
undef $db; # testing to see if we can remove gb
ok( defined($seq = $seqio->next_seq()));
ok( $seq->length, 200);
#swissprot
ok defined($db2 = new Bio::DB::BioFetch( -db => 'swall'));
ok(defined($seq = $db2->get_Seq_by_id('YNB3_YEAST')));
ok( $seq->length, 125);
ok($seq->division, 'YEAST');
$db2->request_format('fasta');
ok(defined($seq = $db2->get_Seq_by_acc('P43780')));
ok($seq->length,103);
};
if ($@) {
if( $DEBUG ) {
print STDERR "Warning: Couldn't connect to EMBL with Bio::DB::EMBL.pm!\n" . $@;
}
foreach ( $Test::ntest..$NUMTESTS) {
skip('No network access - could not connect to embl',1);
}
exit(0);
}
$seq = $seqio = undef;
eval {
$db = new Bio::DB::BioFetch(-retrievaltype => 'tempfile',
-format => 'fasta',
-verbose => $verbose
);
ok( defined($seqio = $db->get_Stream_by_id('J00522 AF303112 J02231')));
ok($seqio->next_seq->length, 408);
ok($seqio->next_seq->length, 1611);
ok($seqio->next_seq->length, 200);
};
if ($@) {
if( $DEBUG ) { warn "Batch access test failed.\nError: $@\n"; }
foreach ( $Test::ntest..$NUMTESTS ) { skip('no network access skipping fasta retrieval',1); }
exit(0);
}
$verbose = -1;
ok $db = new Bio::DB::BioFetch(-db => 'EMBL',
-verbose => $verbose);
eval {
$seq = $db->get_Seq_by_acc('NT_006732');
};
ok $@;
eval {
ok $seq = $db->get_Seq_by_acc('NM_006732');
ok($seq );
ok($seq->length, 3775);
};
if ($@) {
if( $DEBUG ) {
print STDERR "Warning: Couldn't connect to BioFetch server with Bio::DB::BioFetch.pm!\n" . $@;
}
foreach ( $Test::ntest..$NUMTESTS) {
skip('No network aceess - could not connect to embl',1);
}
exit(0);
}
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