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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
# 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;
my $error;
use vars qw($NUMTESTS);
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
$error=0;
use Test;
$NUMTESTS=13;
plan tests => $NUMTESTS;
eval { require IO::String; };
if( $@ ) {
print STDERR "IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests.\n";
for( 1..$NUMTESTS ) {
skip("IO::String not installed",1);
}
$error = 1;
}
}
if( $error == 1 ) {
exit(0);
}
require Bio::LiveSeq::Mutator;
require Bio::LiveSeq::IO::BioPerl;
require Bio::LiveSeq::Gene;
require Bio::Root::IO;
$a = Bio::LiveSeq::Mutator->new();
ok $a;
ok $a->numbering, 'coding';
ok $a->numbering('coding 1');
ok $a->numbering, 'coding 1';
require Bio::LiveSeq::Mutation;
my $mt = new Bio::LiveSeq::Mutation;
ok $mt->seq('g');
$mt->pos(100);
ok ($a->add_Mutation($mt));
my @each = $a->each_Mutation;
ok( (scalar @each), 1 );
my $mt_b = pop @each;
ok($mt_b->seq, 'g');
my $filename=Bio::Root::IO->catfile("t","data","ar.embl");
my $loader=Bio::LiveSeq::IO::BioPerl->load('-file' => "$filename");
my $gene_name='AR'; # was G6PD
my $gene=$loader->gene2liveseq('-gene_name' => $gene_name);
ok($gene);
ok $a->gene($gene);
my $results = $a->change_gene();
ok($results);
eval { require IO::String };
if( $@ ) {
print STDERR "IO::String not installed. Skipping output test.\n";
skip("IO::String not installed",1);
} else {
use Bio::Variation::IO;
require IO::String;
my $s;
my $io = IO::String->new($s);
my $out = Bio::Variation::IO->new('-fh' => $io,
'-format' => 'flat'
);
ok($out->write($results));
#print $s;
ok ($s=~/DNA/ && $s=~/RNA/ && $s=~/AA/);
}
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