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# -*-Perl-*- Test Harness script for Bioperl
# $Id: WithQuality.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 22);
use_ok('Bio::Seq::SeqWithQuality');
use_ok('Bio::PrimarySeq');
use_ok('Bio::Seq::PrimaryQual');
}
my $DEBUG = test_debug();
my $verbosity = $DEBUG || -1;
# create some random sequence object with no id
my $seqobj_broken = Bio::PrimarySeq->new( -seq => "ATCGATCGA");
ok my $seqobj = Bio::PrimarySeq->new( -seq => "ATCGATCGA",
-id => 'QualityFragment-12',
-accession_number => 'X78121',
-verbose => $verbosity);
# 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',
-verbose => $verbosity);
};
ok(!$@);
# check to see what happens when you construct the SeqWithQuality object
my $swq1 = Bio::Seq::SeqWithQuality->new( -seq => $seqobj,
-verbose => $verbosity,
-qual => $qualobj);
ok(!$@);
no warnings;
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,
-verbose => $verbosity,
-qual => "");
};
ok(!$@);
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 => "",
-verbose => $verbosity,
-qual => $qualobj,
-alphabet => 'dna'
);
print("\tc) Absolutely nothing. (HAHAHAHA)...\n") if $DEBUG;
eval {
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
-verbose => $verbosity,
-qual => "",
-alphabet => 'dna'
);
};
ok(!$@);
print("\td) Absolutely nothing but an ID\n") if $DEBUG;
eval {
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
-verbose => $verbosity,
-qual => "",
-alphabet => 'dna',
-id => 'an object with no sequence and no quality but with an id'
);
};
ok(!$@);
print("\td) No sequence, No quality, No ID...\n") if $DEBUG;
eval {
$wswq1 = Bio::Seq::SeqWithQuality->new( -seq => "",
-verbose => $verbosity,
-qual => "");
};
# this should fail without a alphabet
ok($@);
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 = $swq1->seq();
is ($original_seq, "ATCGATCGA");
print("\t1b) set\n") if $DEBUG;
ok ($swq1->seq("AAAAAAAAAAAA"));
print("\t1c) get (again, to make sure the set was done.)\n") if $DEBUG;
is ($swq1->seq(), "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 $str_qual = join(' ',@qual);
is ($str_qual, "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 $str_qual2 = join(' ',@qual2);
is($str_qual2, "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 $DEBUG;
is($swq1->length(), 9);
print("\t3b) When lengths are different\n") if $DEBUG;
$swq1->qual("10 10 10 10 10");
is($swq1->length(), "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();
isa_ok $retr_qual_obj, "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();
isa_ok $retr_seq_obj, "Bio::PrimarySeq";
print("\t5b) Testing seq_obj(\$ref)...\n") if $DEBUG;
$swq1->seq_obj($seqobj);
print("6. Testing the subqual() method...\n") if $DEBUG;
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") if $DEBUG;
# ok ('1 2 3' eq join(' ',@{$swq1->subqual(1,3)}));
print("\t6d) Testing the subqual at the end (border condition)\n") if $DEBUG;
# ok ('7 8 9' eq join(' ',@{$swq1->subqual(7,9)}));
print("\t6d) Testing the subqual in the middle\n") if $DEBUG;
# ok ('4 5 6' eq join(' ',@{$swq1->subqual(4,6)}));
print("7. Testing cases where quality is zero...\n") if $DEBUG;
$swq1 = Bio::Seq::SeqWithQuality->new(-seq => 'G',
-qual => '0',
-verbose => $verbosity,
);
my $swq2 = Bio::Seq::SeqWithQuality->new(-seq => 'G',
-qual => '65',
-verbose => $verbosity,
);
is $swq1->length, $swq2->length;
$swq1 = Bio::Seq::SeqWithQuality->new(-seq => 'GC',
-verbose => $verbosity,
-qual => '0 0',
);
$swq2 = Bio::Seq::SeqWithQuality->new(-seq => 'GT',
-verbose => $verbosity,
-qual => '65 0',
);
is $swq1->length, $swq2->length;
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