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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
use vars qw($NTESTS);
$NTESTS = 17;
plan tests => $NTESTS;
}
use Bio::Root::IO;
use Bio::SeqIO;
use Bio::Cluster::SequenceFamily;
my $seqio= new Bio::SeqIO('-format' => 'swiss',
'-file' => Bio::Root::IO->catfile('t','data','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);
ok $family->description, "SomeFamily";
ok $family->annotation_score,100;
ok $family->size, 5;
ok $family->family_id,"Family_1";
ok $family->version, "1.0";
$family->add_members($mem[0]);
$family->add_members($mem[1]);
ok $family->size, 7;
ok $family->cluster_score, "50";
ok $family->family_score, "50";
my @members = $family->get_members(-ncbi_taxid=>9606);
foreach my $mem(@members){
ok $mem->species->ncbi_taxid, 9606;
}
@members = $family->get_members(-binomial=>"Homo sapiens");
foreach my $mem(@members){
ok $mem->species->binomial, "Homo sapiens";
}
$family->flush_members();
ok $family->size, 0;
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