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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Assembly.t,v 1.2 2002/12/01 00:35:45 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 $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 DB_File };
if( $@ ) {
print STDERR "DB_File not installed. This means the Assembly modules are not available. Skipping tests.\n";
for( 1..$NUMTESTS ) {
skip("DB_File not installed",1);
}
$error = 1;
}
}
END {
foreach ( $Test::ntest..$NUMTESTS) {
skip('unable to run all of the DB tests',1);
}
}
if( $error == 1 ) {
exit(0);
}
#syntax test
require Bio::Assembly::IO;
require Bio::Assembly::Scaffold;
require Bio::Assembly::Contig;
require Bio::Assembly::ContigAnalysis;
use Data::Dumper;
ok 1;
#
# Testing IO
#
# -file => ">".Bio::Root::IO->catfile("t","data","primaryseq.embl")
ok my $in = Bio::Assembly::IO->new
(-file=>Bio::Root::IO->catfile
("t","data","consed_project","edit_dir","test_project.phrap.out"));
ok my $sc = $in->next_assembly;
#print Dumper $sc;
#
# Testing Scaffold
#
ok $sc->id, "NoName";
ok $sc->id('test'), "test";
ok $sc->annotation;
skip "no annotations in Annotation collection?", $sc->annotation->get_all_annotation_keys, 0;
skip "should return a number", $sc->get_nof_contigs, undef ;
ok $sc->get_nof_sequences_in_contigs, 2;
skip "should return a number", $sc->get_nof_singlets, 0;
skip $sc->get_seq_ids, 2;
skip $sc->get_contig_ids, 1;
skip "nothing to test", $sc->get_singlet_ids;
#
# Testing Contig
#
#
# Testing ContigAnalysis
#
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