SENDU / bioperl-1.5.2_005-RCb / t / RefSeq.t 

            

              
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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: RefSeq.t,v 1.12 2005/09/17 02:11:21 bosborne 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; 
                         require LWP::UserAgent; 
                         require HTTP::Request::Common;
                 };
        if( $@ ) {
                for( $Test::ntest..$NUMTESTS ) {
                        skip("IO::String,LWP::UserAgent, or HTTP::Request::Common not installed. This means the Bio::DB::* modules are not usable. Skipping tests",1);
                }
                $error = 1;
        }
}
END {
        for ( $Test::ntest..$NUMTESTS ) {
                skip("Unable to complete RefSeq tests - 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);
}