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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: primaryqual.t,v 1.12 2002/12/19 22:10:34 matsallac Exp $
#
# modeled after the t/Allele.t test script
use strict;
use vars qw($DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'};
my $verbose = -1 unless $DEBUG;
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 => 31;
}
END {
unlink qw(batch_write_qual.qual write_qual.qual);
}
# redirect STDERR to STDOUT
open (STDERR, ">&STDOUT");
use Bio::Root::IO;
use Bio::SeqIO;
use Bio::Seq::SeqWithQuality;
use Bio::Seq::PrimaryQual;
my $string_quals = "10 20 30 40 50 40 30 20 10";
print("Quals are $string_quals\n") if($DEBUG);
my $qualobj = Bio::Seq::PrimaryQual->new( '-qual' => $string_quals,
'-id' => 'QualityFragment-12',
'-accession_number' => 'X78121',
);
ok($qualobj);
ok($qualobj->display_id, 'QualityFragment-12');
ok($qualobj->accession_number, 'X78121');
my @q2 = split/ /,$string_quals;
$qualobj = Bio::Seq::PrimaryQual->new
( '-qual' => \@q2,
'-primary_id' => 'chads primary_id',
'-desc' => 'chads desc',
'-accession_number' => 'chads accession_number',
'-id' => 'chads id'
);
ok($qualobj->primary_id, 'chads primary_id');
my $rqual = $qualobj->qual();
ok(ref($rqual) eq "ARRAY");
my $newqualstring = "50 90 1000 20 12 0 0";
$qualobj->qual($newqualstring);
my $retrieved_quality = $qualobj->qual();
my $retrieved_quality_string = join(' ', @$retrieved_quality);
ok($retrieved_quality_string,$newqualstring);
my @newqualarray = split/ /,$newqualstring;
$qualobj->qual(\@newqualarray);
$retrieved_quality = $qualobj->qual();
$retrieved_quality_string = join(' ',@$retrieved_quality);
ok($retrieved_quality_string,$newqualstring);
eval {
$qualobj->qual("chad");
};
ok($@ =~ /not look healthy/);
eval { $qualobj->qual(""); };
ok(!$@);
eval { $qualobj->qual(" 4"); };
ok(!$@);
ok($qualobj->length(),2 );
$qualobj->qual("10 20 30 40 50 40 30 20 10");
my @subquals = @{$qualobj->subqual(3,6);};
ok(@subquals, 4);
# chad, note to self, evaluate border conditions
ok ("30 20 10" eq join(' ',@{$qualobj->subqual(7,9)}));
my @false_comparator = qw(30 40 70 40);
my @true_comparator = qw(30 40 50 40);
ok(!&compare_arrays(\@subquals,\@true_comparator));
eval { $qualobj->subqual(-1,6); };
ok($@ =~ /EX/ );
eval { $qualobj->subqual(1,6); };
ok(!$@);
eval { $qualobj->subqual(1,9); };
ok(!$@);
eval { $qualobj->subqual(9,1); };
ok($@ =~ /EX/ );
ok($qualobj->display_id() eq "chads id");
$qualobj->display_id("chads new display_id");
ok($qualobj->display_id() eq "chads new display_id");
ok($qualobj->accession_number(), "chads accession_number");
$qualobj->accession_number("chads new accession_number");
ok($qualobj->accession_number(), "chads new accession_number");
ok($qualobj->primary_id(), "chads primary_id");
$qualobj->primary_id("chads new primary_id");
ok($qualobj->primary_id(), "chads new primary_id");
ok($qualobj->desc(), "chads desc");
$qualobj->desc("chads new desc");
ok($qualobj->desc(), "chads new desc");
ok($qualobj->display_id(), "chads new display_id");
$qualobj->display_id("chads new id");
ok($qualobj->display_id(), "chads new id");
my $in_qual = Bio::SeqIO->new(-file => "<" . Bio::Root::IO->catfile("t","data","qualfile.qual") ,
'-format' => 'qual',
'-verbose' => $verbose);
ok($in_qual);
my $pq = $in_qual->next_seq();
ok($pq->qual()->[99], '39'); # spot check boundary
ok($pq->qual()->[100], '39'); # spot check boundary
my $out_qual = Bio::SeqIO->new('-file' => ">write_qual.qual",
'-format' => 'qual',
'-verbose' => $verbose);
$out_qual->write_seq(-source => $pq);
my $swq545 = Bio::Seq::SeqWithQuality->new ( -seq => "ATA",
-qual => $pq
);
$out_qual->write_seq(-source => $swq545);
$in_qual = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile("t","data","qualfile.qual") ,
'-format' => 'qual',
'-verbose' => $verbose);
my $out_qual2 = Bio::SeqIO->new('-file' => ">batch_write_qual.qual",
'-format' => 'qual',
'-verbose' => $verbose);
while ( my $batch_qual = $in_qual->next_seq() ) {
$out_qual2->write_seq(-source => $batch_qual);
}
sub display {
if($DEBUG ) {
my @quals;
print("I saw these in qualfile.qual:\n") ;
while ( my $qual = $in_qual->next_seq() ) {
# ::dumpValue($qual);
print($qual->display_id()."\n");
@quals = @{$qual->qual()};
print("(".scalar(@quals).") quality values.\n");
}
}
}
# dumpValue($qualobj);
sub compare_arrays {
my ($a1,$a2) = @_;
return 1 if (scalar(@{$a1}) != scalar(@{$a2}));
my ($v1,$v2,$diff,$curr);
for ($curr=0;$curr<scalar(@{$a1});$curr++){
return 1 if ($a1->[$curr] ne $a2->[$curr]);
}
return 0;
}
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