t/Lagan.t

   1 #!/usr/local/bin/perl
   2 #-*-Perl-*-
   3 # ## Bioperl Test Harness Script for Modules
   4 # #
   5 use strict;
   6 BEGIN {
   7    use Bio::Root::Test;
   8    test_begin(-tests => 12);
   9    use_ok('Bio::AlignIO');
  10    use_ok('Bio::Tools::Run::Alignment::Lagan');
  11    use_ok('Bio::Root::IO');
  12    use_ok('Bio::SeqIO');
  13    use_ok('Bio::Seq');
  14    use_ok('Bio::Matrix::Mlagan');
  15 }
  16
  17 my $seq1 =  test_input_file("lagan_dna.fa");
  18 my $sio = Bio::SeqIO->new(-file=>$seq1,-format=>'fasta');
  19
  20 my $seq = $sio->next_seq;
  21 $seq->id("first_seq");
  22 my $seq2= Bio::Seq->new(-id=>"second_seq",-seq=>$seq->seq);
  23 my $seq3= Bio::Seq->new(-id=>"third_seq",-seq=>$seq->seq);
  24
  25 my @params =
  26              (
  27               'order' => "\"-gs -7 -gc -2 -mt 2 -ms -1\"",
  28               'tree' => "\"(first_seq (second_seq third_seq))\"",
  29               'match' => 12,
  30               'mismatch' => -8,
  31               'gapstart' => -50,
  32               'gapend' => -50,
  33               'gapcont' => -2,
  34          );
  35
  36 SKIP: {
  37    my  $factory = Bio::Tools::Run::Alignment::Lagan->new(@params,
  38                                                          -verbose => -1);
  39    $factory->quiet(1);
  40    isa_ok $factory,'Bio::Tools::Run::Alignment::Lagan';
  41    test_skip(-requires_executable => $factory,
  42              -tests => 5,
  43              -requires_env => 'LAGAN_DIR');
  44
  45    my $simple_align= $factory->lagan($seq,$seq2);
  46
  47    isa_ok $simple_align, 'Bio::SimpleAlign';
  48
  49    is $simple_align->percentage_identity, 100;
  50
  51    my $multi = $factory->mlagan([$seq,$seq2,$seq3]);
  52    is $multi->percentage_identity, 100;
  53
  54    my $matrix = Bio::Matrix::Mlagan->new(-values => [[qw(115 -161 -81 -161 0 -72)],
  55                                                      [qw(-161 115 -161 -81 0 -72)],
  56                                                      [qw(-81 -161 115 -161 0 -72)],
  57                                                      [qw(-161 -81 -161 115 0 -72)],
  58                                                      [qw(0 0 0 0 0 0)],
  59                                                      [qw(-72 -72 -72 -72 0 -72)]],
  60                                          -gap_open => -470,
  61                                          -gap_continue => -25);
  62
  63    is $factory->nuc_matrix($matrix), $matrix;
  64    #*** weak test; doesn't show the supplied matrix had any effect on results...
  65    $multi = $factory->mlagan([$seq,$seq2,$seq3]);
  66    is $multi->percentage_identity, 100;
  67 }