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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: lucy.t,v 1.2 2002/03/07 04:08:04 jason Exp $
use strict;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 22;
}
use Bio::Tools::Lucy;
use Bio::Root::IO;
ok(1);
my @params = (adv_stderr => 1, seqfile => Bio::Root::IO->catfile("t","data","lucy.seq"), rev_desig => 'R');
# Bio::Tools::Lucy will find .qual, .info, and .stderr files in this folder
my $lucyObj = Bio::Tools::Lucy->new(@params);
ok $lucyObj->isa('Bio::Tools::Lucy');
ok $lucyObj->seqfile();
$lucyObj->adv_stderr(1);
my $stderr = $lucyObj->adv_stderr();
ok $stderr;
my $names =$lucyObj->get_sequence_names();
ok $names;
my $seq = shift @$names;
ok $seq, 'TaLr1010B10R';
ok $lucyObj->length_raw("$seq"), 1060;
ok $lucyObj->length_clear("$seq"), 420;
ok $lucyObj->start_clear("$seq"), 86;
ok $lucyObj->end_clear("$seq"), 505;
ok $lucyObj->avg_quality("$seq");
ok $lucyObj->full_length("$seq");
ok $lucyObj->polyA("$seq");
ok $lucyObj->direction("$seq"), 'R';
ok $lucyObj->per_GC("$seq");
ok $lucyObj->sequence("$seq");
ok $lucyObj->quality("$seq");
my $seqObj = $lucyObj->get_Seq_Obj("$seq");
ok $seqObj;
my $seqObjs = $lucyObj->get_Seq_Objs();
ok $seqObjs;
my $rejects = $lucyObj->get_rejects();
ok $rejects;
my ($key) = (sort keys %$rejects);
ok $key, 'TaLr1011A07R';
ok $rejects->{$key}, 'Q';
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