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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 67);
use_ok('Bio::SeqIO');
use_ok('Bio::Seq::Quality');
use_ok('Bio::Seq::PrimaryQual');
}
my $DEBUG = test_debug();
my $verbose = -1 unless $DEBUG;
# redirect STDERR to STDOUT
open (STDERR, ">&STDOUT");
my $string_quals = "10 20 30 40 50 40 30 20 10";
print("Quals are $string_quals\n") if($DEBUG);
ok my $qualobj = Bio::Seq::PrimaryQual->new(
-qual => $string_quals,
-id => 'QualityFragment-12',
-accession_number => 'X78121',
);
is $qualobj->display_id, 'QualityFragment-12';
is $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',
-header => 'chads header'
);
is $qualobj->primary_id, 'chads primary_id';
isa_ok $qualobj->qual(), 'ARRAY';
my $newqualstring = "50 90 1000 20 12 0 0";
ok $qualobj->qual($newqualstring);
is join(' ', @{$qualobj->qual()}), $newqualstring;
my @newqualarray = split / /,$newqualstring;
ok $qualobj->qual(\@newqualarray);
is join(' ', @{$qualobj->qual()}), $newqualstring;
is $qualobj->validate_qual($string_quals), 1;
is $qualobj->validate_qual("" ), 1;
is $qualobj->validate_qual("0" ), 1;
is $qualobj->validate_qual(undef ), 1;
is $qualobj->validate_qual("10 20 30 30"), 1;
is $qualobj->validate_qual(" 20 9.3 5 "), 1;
is $qualobj->validate_qual(" 4" ), 1;
is $qualobj->validate_qual("chad" ), 0;
is $qualobj->validate_qual(" " ), 0;
ok $qualobj->qual("10 20 30 30");
throws_ok { $qualobj->qual("chad"); } qr/.+/;
throws_ok { $qualobj->validate_qual("chad", 1) } qr/.+/;
ok $qualobj->qual("4 10");
is $qualobj->length(), 2;
$qualobj->qual("10 20 30 40 50 40 30 20 10");
ok my @subquals = @{$qualobj->subqual(3,6);};
is @subquals, 4;
is "30 20 10", join(' ',@{$qualobj->subqual(7,9)});
throws_ok { $qualobj->subqual(-1,6); } qr/EX/;
ok $qualobj->subqual(1,6);
ok $qualobj->subqual(1,9);
throws_ok { $qualobj->subqual(9,1); } qr/EX/;
is $qualobj->display_id(), "chads id";
is $qualobj->display_id("chads new display_id"), "chads new display_id";
is $qualobj->display_id(), "chads new display_id";
is $qualobj->accession_number(), "chads accession_number";
is $qualobj->accession_number("chads new accession_number"), "chads new accession_number";
is $qualobj->accession_number(), "chads new accession_number";
is $qualobj->primary_id(), "chads primary_id";
is $qualobj->primary_id("chads new primary_id"), "chads new primary_id";
is $qualobj->primary_id(), "chads new primary_id";
is $qualobj->desc(), "chads desc";
is $qualobj->desc("chads new desc"), "chads new desc";
is $qualobj->desc(), "chads new desc";
is $qualobj->display_id(), "chads new display_id";
is $qualobj->display_id("chads new id"), ("chads new id");
is $qualobj->display_id(), "chads new id";
is $qualobj->header(), "chads header";
ok my $in_qual = Bio::SeqIO->new(
-file => test_input_file('qualfile.qual'),
-format => 'qual',
-verbose => $verbose,
);
ok my $pq = $in_qual->next_seq();
is $pq->qual()->[99] , '39'; # spot check boundary
is $pq->qual()->[100], '39'; # spot check boundary
ok my $out_qual = Bio::SeqIO->new(
-file => ">".test_output_file(),
-format => 'qual',
-verbose => $verbose,
);
ok $out_qual->write_seq(-source => $pq);
ok my $swq545 = Bio::Seq::Quality->new (
-seq => "ATA",
-qual => $pq
);
ok $out_qual->write_seq(-source => $swq545);
ok $in_qual = Bio::SeqIO->new(
-file => test_input_file('qualfile.qual'),
-format => 'qual',
-verbose => $verbose,
);
ok my $out_qual2 = Bio::SeqIO->new(
-file => ">".test_output_file(),
-format => 'qual',
-verbose => $verbose,
);
while ( my $batch_qual = $in_qual->next_seq() ) {
ok $out_qual2->write_seq(-source => $batch_qual);
}
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