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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: seqwithquality.t,v 1.6 2002/12/19 22:10:34 matsallac Exp $
use strict;
use Dumpvalue;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 18;
}
my $dumper = new Dumpvalue();
my $DEBUG = $ENV{'BIOPERLDEBUG'};
# redirect STDERR to STDOUT
open (STDERR, ">&STDOUT");
print("Checking if the Bio::Seq::SeqWithQuality module could be used...\n") if $DEBUG;
# test 1
use Bio::Seq::SeqWithQuality;
ok(1);
use Bio::PrimarySeq;
use Bio::Seq::PrimaryQual;
# create some random sequence object with no id
my $seqobj_broken = Bio::PrimarySeq->new( -seq => "ATCGATCGA",
);
# dumpValue($seqobj_broken);
my $seqobj = Bio::PrimarySeq->new( -seq => "ATCGATCGA",
-id => 'QualityFragment-12',
-accession_number => 'X78121',
);
ok(!$@);
# create some random quality object with the same number of qualities and the same identifiers
my $string_quals = "10 20 30 40 50 40 30 20 10";
my $indices = "5 10 15 20 25 30 35 40 45";
my $qualobj;
eval {
$qualobj = Bio::Seq::PrimaryQual->new( -qual => $string_quals,
-id => 'QualityFragment-12',
-accession_number => 'X78121',
);
};
ok(!$@);
# check to see what happens when you construct the SeqWithQuality object
my $swq1 = Bio::Seq::SeqWithQuality->new( -seq => $seqobj,
-qual => $qualobj);
ok(!$@);
print("Testing various weird constructors...\n") if $DEBUG;
print("\ta) No ids, Sequence object, no quality...\n") if $DEBUG;
# w for weird
my $wswq1;
eval {
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => $seqobj,
-qual => "");
};
ok(!$@);
print("\tb) No ids, no sequence, quality object...\n") if $DEBUG;
# note that you must provide a alphabet for this one.
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
-qual => $qualobj,
-alphabet => 'dna'
);
print("\tc) Absolutely nothing. (HAHAHAHA)...\n") if $DEBUG;
eval {
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
-qual => "",
-alphabet => 'dna'
);
};
ok(!$@);
print("\td) Absolutely nothing but an ID\n") if $DEBUG;
eval {
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
-qual => "",
-alphabet => 'dna',
-id => 'an object with no sequence and no quality but with an id'
);
};
ok(!$@);
print("\td) No sequence, No quality, No ID...\n") if $DEBUG;
eval {
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
-qual => "");
};
# this should fail without a alphabet
ok($@);
# dumpValue($wswq1);
print("Testing various methods and behaviors...\n") if $DEBUG;
print("1. Testing the seq() method...\n") if $DEBUG;
print("\t1a) get\n") if $DEBUG;
my $original_seq = $swq1->seq();
ok ($original_seq eq "ATCGATCGA");
print("\t1b) set\n") if $DEBUG;
ok ($swq1->seq("AAAAAAAAAAAA"));
print("\t1c) get (again, to make sure the set was done.)\n") if $DEBUG;
ok($swq1->seq() eq "AAAAAAAAAAAA");
print("\tSetting the sequence back to the original value...\n") if $DEBUG;
$swq1->seq($original_seq);
print("2. Testing the qual() method...\n") if $DEBUG;
print("\t2a) get\n") if $DEBUG;
my @qual = @{$swq1->qual()};
my $str_qual = join(' ',@qual);
ok ($str_qual eq "10 20 30 40 50 40 30 20 10");
print("\t2b) set\n") if $DEBUG;
ok ($swq1->qual("10 10 10 10 10"));
print("\t2c) get (again, to make sure the set was done.)\n") if $DEBUG;
my @qual2 = @{$swq1->qual()};
my $str_qual2 = join(' ',@qual2);
ok($str_qual2 eq "10 10 10 10 10");
print("\tSetting the quality back to the original value...\n") if $DEBUG;
$swq1->qual($str_qual);
print("3. Testing the length() method...\n") if $DEBUG;
print("\t3a) When lengths are equal...\n") if $DEBUG;
ok($swq1->length() == 9);
print("\t3b) When lengths are different\n") if $DEBUG;
$swq1->qual("10 10 10 10 10");
# why is this test failing?
# dumpValue($swq1);
ok($swq1->length() eq "DIFFERENT");
print("4. Testing the qual_obj() method...\n") if $DEBUG;
print("\t4a) Testing qual_obj()...\n") if $DEBUG;
my $retr_qual_obj = $swq1->qual_obj();
ok (ref($retr_qual_obj) eq "Bio::Seq::PrimaryQual");
print("\t4b) Testing qual_obj(\$ref)...\n") if $DEBUG;
$swq1->qual_obj($qualobj);
print("5. Testing the seq_obj() method...\n") if $DEBUG;
print("\t5a) Testing seq_qual_obj()...\n") if $DEBUG;
my $retr_seq_obj = $swq1->seq_obj();
ok (ref($retr_seq_obj) eq "Bio::PrimarySeq");
print("\t5b) Testing seq_obj(\$ref)...\n") if $DEBUG;
$swq1->seq_obj($seqobj);
print("6. Testing the subqual() method...\n");
my $t_subqual = "10 20 30 40 50 60 70 80 90";
$swq1->qual($t_subqual);
print("\t6d) Testing the subqual at the start (border condition)\n");
# ok ('1 2 3' eq join(' ',@{$swq1->subqual(1,3)}));
print("\t6d) Testing the subqual at the end (border condition)\n");
# ok ('7 8 9' eq join(' ',@{$swq1->subqual(7,9)}));
print("\t6d) Testing the subqual in the middle\n");
# ok ('4 5 6' eq join(' ',@{$swq1->subqual(4,6)}));
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