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SENDU / bioperl-1.5.2_004-RCe / t / MapIO.t 

            

              
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# -*-Perl-*-
# Bioperl Test Harness Script for Modules
# $Id: MapIO.t,v 1.4.4.3 2006/10/02 23:10:40 sendu Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
my $error = 0;
use strict;
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; };
        if( $@ ) {
                use lib 't';
        }
        use Test;
        plan tests => 51; 
}
if( $error == 1 ) {
        exit(0);
}
use Bio::MapIO;
use Bio::Root::IO;
my $verbose = $ENV{'BIOPERLDEBUG'};
ok 1;
ok my $mapio = new Bio::MapIO(-verbose => $verbose,
                                                                                -format => 'mapmaker',
                                                                                -file   => Bio::Root::IO->catfile
                                                                                ('t','data','mapmaker.out'));
my $map = $mapio->next_map;
ok(ref($map) && $map->isa('Bio::Map::MapI'));
ok $map->units, 'cM';
ok $map->type, 'Genetic';
ok $map->name('test map'), 'test map'; # map name is unset for this data type
my $count;
foreach my $marker ( $map->each_element ) {
        $count++;
        ok($marker->position->order,$count);
}
ok $count,18;
ok $mapio = new Bio::MapIO(-format => 'mapmaker',
                                                                        -file   => Bio::Root::IO->catfile
                                                                        ('t','data','mapmaker.txt'));
$map = $mapio->next_map;
ok $map->length,382.5;
$count = 0;
foreach my $marker ( $map->each_element ) {
        $count++;
        ok($marker->position->order,$count);
}
ok $count,13;
ok $mapio = Bio::MapIO->new(-format => 'fpc',
                                                                        -file   => Bio::Root::IO->catfile
                                                                        ('t','data','ctgdemo.fpc'));
$map = $mapio->next_map;
ok($map->length, 0);
ok($map->version, 7.2);
ok($map->modification_user, 'cari');
ok($map->group_type, 'Chromosome');
ok($map->group_abbr, 'Chr');
ok($map->core_exists, 0);
$count = 0;
foreach my $marker ($map->each_markerid) {
        $count++;
}
ok($count,150);
# add tests for get_markerobj
$count = 0;
foreach my $clone ($map->each_cloneid) {
        $count++;
}
ok($count,618);
# add tests for get_cloneobj
$count = 0;
foreach my $contig ($map->each_contigid) {
        $count++;
}
ok($count,2);
# add tests for get_contigobj
# need tests for
# matching_bands
# coincidence_score
# print_contiglist
# print_markerlist
# print_gffstyle