t/ClusterIO/SequenceFamily.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           => 17,
  11                -requires_module => 'Data::Stag');
  12
  13     use_ok('Bio::SeqIO');
  14     use_ok('Bio::Cluster::SequenceFamily');
  15 }
  16
  17 my $seqio= Bio::SeqIO->new('-format' => 'swiss',
  18                            '-file'   => test_input_file('sequencefamily.dat'));
  19 my @mem;
  20 while(my $seq = $seqio->next_seq){
  21     push @mem, $seq;
  22 }
  23 my $family = Bio::Cluster::SequenceFamily->new(
  24     -family_id=>"Family_1",
  25     -description=>"SomeFamily",
  26     -annotation_score=>"100",
  27     -family_score=>"50",
  28     -version=>"1.0",
  29     -members=>\@mem,
  30 );
  31 is $family->description, "SomeFamily";
  32 is $family->annotation_score,100;
  33 is $family->size, 5;
  34 is $family->family_id,"Family_1";
  35 is $family->version, "1.0";
  36
  37 $family->add_members($mem[0]);
  38 $family->add_members($mem[1]);
  39 is $family->size, 7;
  40 is $family->cluster_score, "50";
  41 is $family->family_score, "50";
  42
  43 my @members = $family->get_members(-ncbi_taxid=>9606);
  44
  45 foreach my $mem(@members){
  46     is $mem->species->ncbi_taxid, 9606;
  47 }
  48
  49 @members = $family->get_members(-binomial=>"Homo sapiens");
  50
  51 foreach my $mem(@members){
  52     is $mem->species->binomial, "Homo sapiens";
  53 }
  54
  55
  56 $family->flush_members();
  57
  58 is $family->size, 0;