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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: RefSeq.t,v 1.10 2003/12/18 10:35:24 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;
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 = 13;
plan tests => $NUMTESTS;
eval { require 'IO/String.pm' };
if( $@ ) {
for( $Test::ntest..$NUMTESTS ) {
skip("IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests",1);
}
$error = 1;
}
}
END {
for ( $Test::ntest..$NUMTESTS ) {
skip("Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test",1);
}
}
if( $error == 1 ) {
exit(0);
}
require Bio::DB::RefSeq;
require Bio::DB::GenBank;
require Bio::DB::EMBL;
my $testnum;
my $verbose = 0;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my ($db,$seq,$db2,$seq2,$seqio);
# get a single seq
$seq = $seqio = undef;
#test redirection from GenBank and EMBL
$verbose = -1;
#GenBank
ok $db = new Bio::DB::GenBank('-verbose'=>$verbose) ;
#EMBL
ok $db2 = new Bio::DB::EMBL('-verbose'=>$verbose) ;
eval {
$seq = $db->get_Seq_by_acc('NT_006732');
$seq2 = $db2->get_Seq_by_acc('NT_006732');
};
ok $@;
exit unless $DEBUG;
eval {
ok($seq = $db->get_Seq_by_acc('NM_006732'));
ok($seq && $seq->length eq 3775);
ok $seq2 = $db2->get_Seq_by_acc('NM_006732');
ok($seq2 && $seq2->length eq 3775);
};
if ($@) {
if( $DEBUG ) {
print STDERR "Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!\n" . $@;
}
exit(0);
}
$verbose = 0;
eval {
ok defined($db = new Bio::DB::RefSeq(-verbose=>$verbose));
ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
ok( $seq->length, 3775);
ok defined ($db->request_format('fasta'));
ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
ok( $seq->length, 3775);
};
if ($@) {
if( $DEBUG ) {
print STDERR "Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!\n" . $@;
}
exit(0);
}
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