t/SequenceFamily.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib 't/lib';
   8     use BioperlTest;
   9
  10     test_begin(-tests => 19);
  11
  12     use_ok('Bio::SeqIO');
  13     use_ok('Bio::Cluster::SequenceFamily');
  14 }
  15
  16 my $seqio= Bio::SeqIO->new('-format' => 'swiss',
  17                            '-file'   => test_input_file('sequencefamily.dat'));
  18 my @mem;
  19 while(my $seq = $seqio->next_seq){
  20     push @mem, $seq;
  21 }
  22 my $family = Bio::Cluster::SequenceFamily->new(-family_id=>"Family_1",
  23                                        -description=>"SomeFamily",
  24                                        -annotation_score=>"100",
  25                                        -family_score=>"50",
  26                                        -version=>"1.0",
  27                                        -members=>\@mem);
  28 is $family->description, "SomeFamily";
  29 is $family->annotation_score,100;
  30 is $family->size, 5;
  31 is $family->family_id,"Family_1";
  32 is $family->version, "1.0";
  33
  34 $family->add_members($mem[0]);
  35 $family->add_members($mem[1]);
  36 is $family->size, 7;
  37 is $family->cluster_score, "50";
  38 is $family->family_score, "50";
  39
  40 my @members = $family->get_members(-ncbi_taxid=>9606);
  41
  42 foreach my $mem(@members){
  43     is $mem->species->ncbi_taxid, 9606;
  44 }
  45
  46 @members = $family->get_members(-binomial=>"Homo sapiens");
  47
  48 foreach my $mem(@members){
  49     is $mem->species->binomial, "Homo sapiens";
  50 }
  51
  52
  53 $family->flush_members();
  54
  55 is $family->size, 0;