t/SeqEvolution.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 39);
  11
  12     use_ok('Bio::SeqEvolution::Factory');
  13     use_ok('Bio::PrimarySeq');
  14 }
  15
  16 #
  17 # point mutations
  18 #
  19
  20 ok my $evolve = Bio::SeqEvolution::Factory->new (-verbose => 1);
  21 isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';
  22
  23 ok $evolve = Bio::SeqEvolution::DNAPoint->new (-verbose => 2);
  24 isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';
  25
  26 ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 3,
  27                                              -type => 'Bio::SeqEvolution::DNAPoint');
  28 isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';
  29
  30
  31 my $seq = Bio::PrimarySeq->new(-id=>'test',
  32                               -seq=>'aaacccgggtta'
  33                              );
  34
  35 ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
  36                                               -foo => 'bar',
  37                                               -rate => 5,
  38                                               -seq => $seq
  39                                              );
  40
  41 is $evolve->seq->id, 'test';
  42 is $evolve->rate, 5,               'get rate()';
  43 is $evolve->rate(2), 2,            'get and set rate()';
  44
  45
  46 is $evolve->identity(80), 80, 'identity()';
  47 is $evolve->identity(undef), undef, 'identity()';
  48
  49 is $evolve->pam, undef, 'pam()';
  50 is $evolve->pam(80), 80, 'pam()';
  51
  52 is $evolve->mutation_count, undef, 'mutation_count()';
  53 is $evolve->mutation_count(5), 5, , 'mutation_count()';
  54
  55
  56
  57 is $evolve->seq_type, 'Bio::PrimarySeq', 'seq_type()';
  58 is $evolve->seq_type('Bio::Seq'), 'Bio::Seq', 'seq_type()';
  59
  60 ok my $newseq = $evolve->next_seq, 'next_seq()';
  61
  62 foreach ( $evolve->each_mutation('string')) {
  63     ok $_;
  64 }
  65 is $evolve->each_mutation, 5, 'each_mutation()';
  66
  67 ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
  68                                               -rate => 5,
  69                                               -seq => $seq,
  70                                               -identity => 50     ###
  71                                              );
  72 ok $newseq = $evolve->next_seq;
  73 cmp_ok $evolve->get_alignment_identity, '<=', 50, "get_alignment_identity()";
  74
  75 ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
  76                                               -rate => 5,
  77                                               -seq => $seq,
  78                                               -pam => 50     ###
  79                                              );
  80 ok $newseq = $evolve->next_seq;
  81 is $evolve->get_mutation_counter, 6, 'get_mutation_counter()';
  82 $newseq = $evolve->next_seq;
  83 is $evolve->get_sequence_counter, 2, 'get_sequence_counter()';
  84 ok $evolve->reset_sequence_counter(), 'reset_sequence_counter()';
  85 is $evolve->get_sequence_counter, 0, 'get_sequence_counter() == 0';
  86
  87 ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
  88                                               -rate => 5,
  89                                               -seq => $seq,
  90                                               -pam => 50
  91                                              );
  92
  93 ok $newseq = $evolve->next_seq;
  94 # ok $evolve->get_alignment_identity <= 50, "get_alignment_identity()";
  95 isa_ok $evolve->get_alignmet, 'Bio::SimpleAlign';
  96
  97
  98 #
  99 #print "-----------------------------------------\n";
 100 #print $evolve->{'_ori_locatableseq'}->seq, "\n";
 101 #print $evolve->{'_mut_locatableseq'}->seq, "\n";
 102 #print $evolve->{'_align'}->overall_percentage_identity, "\n";
 103 #print $evolve->get_mutation_counter, "\n";
 104 #print "-----------------------------------------\n";
 105 #
 106
 107
 108 #
 109 # indels
 110 #
 111
 112 #use Bio::SeqEvolution::DNAIndel;
 113 #ok $evolve = Bio::SeqEvolution::DNAIndel->new (-verbose => 0,
 114 #                                               -mutation_count => 3,
 115 #                                               -rate => 1,
 116 #                                               -seq => $seq
 117 #                                             );
 118 #
 119 #
 120 #
 121 #ok $newseq = $evolve->next_seq;
 122 #ok $evolve->get_mutation_counter, 3;
 123 ##print Dumper $evolve;
 124 #
 125 #foreach ( $evolve->each_mutation) {
 126 ##    print Dumper $_;
 127 ##    print $_->sysname, "\n";
 128 #    ok $_->sysname;
 129 #}
 130 #
 131 #
 132 #ok $evolve = Bio::SeqEvolution::DNAIndel->new (-verbose => 0,
 133 #                                               -duplication => 1,
 134 ##                                               -identity =>50,
 135 #                                               -mutation_count => 3,
 136 #                                               -rate => 1,
 137 #                                               -seq => $seq
 138 #                                             );
 139 ##$evolve->{'_mut_string'} = $evolve->{'_ori_string'};
 140 #
 141 ##ok $newseq = $evolve->mutate(12);
 142 #ok $newseq = $evolve->next_seq;
 143 ##print Dumper $evolve;
 144 ##print $evolve->{'_ori_locatableseq'}->seq, "\n";
 145 ##print $evolve->{'_mut_locatableseq'}->seq, "\n";
 146 #
 147 #print "-----------------------------------------\n";
 148 #print $evolve->{'_ori_locatableseq'}->seq, "\n";
 149 #print $evolve->{'_mut_locatableseq'}->seq, "\n";
 150 #print $evolve->{'_align'}->overall_percentage_identity, "\n";
 151 #print "-----------------------------------------\n";
 152 #
 153 #
 154 ##
 155 ## mixer, simulation
 156 ##
 157 #
 158 #
 159 #ok my $evolve2 = Bio::SeqEvolution::Factory->new (-verbose => 0,
 160 #                                                  -rate => 2,
 161 #                                                  -seq => $seq,
 162 #                                                  -set_mutated_seq => $newseq,
 163 ##                                                  -identity => 50
 164 #                                                  -mutation_count => 1     ###
 165 #                                             );
 166 #ok $evolve2->seq_type('Bio::LocatableSeq');
 167 #
 168 #print "=-----------------------------------------\n";
 169 #print $evolve2->{'_ori_locatableseq'}->seq, "\n";
 170 #print $evolve2->{'_mut_locatableseq'}->seq, "\n";
 171 #print $evolve2->{'_align'}->overall_percentage_identity, "\n";
 172 #print "-----------------------------------------\n";
 173 #
 174 #ok $newseq = $evolve2->next_seq;
 175 #
 176 #
 177 #print "-----------------------------------------\n";
 178 #print $evolve2->{'_ori_locatableseq'}->seq, "\n";
 179 #print $evolve2->{'_mut_locatableseq'}->seq, "\n";
 180 #print $evolve2->{'_align'}->overall_percentage_identity, "\n";
 181 #print "-----------------------------------------\n";
 182 #