2 ## Bioperl Test Harness Script for Modules
5 use vars qw($NUMTESTS);
7 eval { require Test; };
14 plan tests => $NUMTESTS;
17 END { unlink qw(cysprot.dnd cysprot1a.dnd) }
19 use Bio::Tools::Run::Alignment::Kalign;
25 for ( $Test::ntest..$NUMTESTS ) {
26 skip("Kalign program not found. Skipping.\n",1);
33 my $factory = Bio::Tools::Run::Alignment::Kalign->new(@params);
34 my $inputfilename = Bio::Root::IO->catfile("t","data","cysprot.fa");
37 my $present = $factory->executable();
38 unless ($present && -e $present ) {
39 warn "amap program not found. Skipping tests $Test::ntest to $NUMTESTS.\n";
42 my $version = $factory->version;
43 ok ($version >= 2, 1, "Code tested only on kalign versions >= 2" );
44 $aln = $factory->align($inputfilename);
46 ok( $aln->no_sequences, 7);
48 my $str = Bio::SeqIO->new('-file' =>
49 Bio::Root::IO->catfile("t","data","cysprot.fa"),
50 '-format' => 'Fasta');
53 while ( my $seq = $str->next_seq() ) {
54 push (@seq_array, $seq) ;
57 my $seq_array_ref = \@seq_array;
59 $aln = $factory->align($seq_array_ref);
60 ok $aln->no_sequences, 7;
61 my $s1_perid = $aln->average_percentage_identity;
62 ok(int($s1_perid), 42);