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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 17,
-requires_module => 'Data::Stag');
use_ok('Bio::SeqIO');
use_ok('Bio::Cluster::SequenceFamily');
}
my $seqio= Bio::SeqIO->new('-format' => 'swiss',
'-file' => test_input_file('sequencefamily.dat'));
my @mem;
while(my $seq = $seqio->next_seq){
push @mem, $seq;
}
my $family = Bio::Cluster::SequenceFamily->new(
-family_id=>"Family_1",
-description=>"SomeFamily",
-annotation_score=>"100",
-family_score=>"50",
-version=>"1.0",
-members=>\@mem,
);
is $family->description, "SomeFamily";
is $family->annotation_score,100;
is $family->size, 5;
is $family->family_id,"Family_1";
is $family->version, "1.0";
$family->add_members($mem[0]);
$family->add_members($mem[1]);
is $family->size, 7;
is $family->cluster_score, "50";
is $family->family_score, "50";
my @members = $family->get_members(-ncbi_taxid=>9606);
foreach my $mem(@members){
is $mem->species->ncbi_taxid, 9606;
}
@members = $family->get_members(-binomial=>"Homo sapiens");
foreach my $mem(@members){
is $mem->species->binomial, "Homo sapiens";
}
$family->flush_members();
is $family->size, 0;
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