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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 109);
use_ok('Bio::Location::Simple');
use_ok('Bio::Location::Split');
use_ok('Bio::Location::Fuzzy');
use_ok('Bio::SeqFeature::Generic');
use_ok('Bio::SeqFeature::SimilarityPair');
use_ok('Bio::SeqFeature::FeaturePair');
use_ok('Bio::SeqFeature::Lite');
}
my $simple = Bio::Location::Simple->new('-start' => 10, '-end' => 20,
'-strand' => 1, -seq_id => 'my1');
isa_ok($simple, 'Bio::LocationI');
isa_ok($simple, 'Bio::RangeI');
is($simple->start, 10, 'Bio::Location::Simple tests');
is($simple->end, 20);
is($simple->seq_id, 'my1');
my ($loc) = $simple->each_Location();
ok($loc);
is("$loc", "$simple");
my $generic = Bio::SeqFeature::Generic->new('-start' => 5, '-end' => 30,
'-strand' => 1);
isa_ok($generic,'Bio::SeqFeatureI', 'Bio::SeqFeature::Generic' );
isa_ok($generic,'Bio::RangeI');
is($generic->start, 5);
is($generic->end, 30);
my $lite_pos = Bio::SeqFeature::Lite->new(-start => 1000, -stop => 2000, -strand => '+');
my $lite_neg = Bio::SeqFeature::Lite->new(-start => 1000, -end => 2000, -strand => '-');
my $lite_none = Bio::SeqFeature::Lite->new(-start => 1000, -stop => 2000, -strand => '.');
is($lite_pos->strand, 1);
is($lite_neg->strand, -1);
is($lite_neg->end, 2000);
is($lite_neg->stop, 2000);
is($lite_none->strand, 0);
my $similarity = Bio::SeqFeature::SimilarityPair->new();
my $feat1 = Bio::SeqFeature::Generic->new('-start' => 30, '-end' => 43,
'-strand' => -1);
my $feat2 = Bio::SeqFeature::Generic->new('-start' => 80, '-end' => 90,
'-strand' => -1);
my $featpair = Bio::SeqFeature::FeaturePair->new('-feature1' => $feat1,
'-feature2' => $feat2 );
my $feat3 = Bio::SeqFeature::Generic->new('-start' => 35, '-end' => 50,
'-strand' => -1);
is($featpair->start, 30,'Bio::SeqFeature::FeaturePair tests');
is($featpair->end, 43);
is($featpair->length, 14);
ok($featpair->overlaps($feat3));
ok($generic->overlaps($simple), 'Bio::SeqFeature::Generic tests');
ok($generic->contains($simple));
# fuzzy location tests
my $fuzzy = Bio::Location::Fuzzy->new('-start' =>'<10',
'-end' => 20,
-strand =>1,
-seq_id =>'my2');
is($fuzzy->strand, 1, 'Bio::Location::Fuzzy tests');
is($fuzzy->start, 10);
is($fuzzy->end,20);
ok(!defined $fuzzy->min_start);
is($fuzzy->max_start, 10);
is($fuzzy->min_end, 20);
is($fuzzy->max_end, 20);
is($fuzzy->location_type, 'EXACT');
is($fuzzy->start_pos_type, 'BEFORE');
is($fuzzy->end_pos_type, 'EXACT');
is($fuzzy->seq_id, 'my2');
is($fuzzy->seq_id('my3'), 'my3');
($loc) = $fuzzy->each_Location();
ok($loc);
is("$loc", "$fuzzy");
# split location tests
my $splitlocation = Bio::Location::Split->new();
my $f = Bio::Location::Simple->new(-start => 13,
-end => 30,
-strand => 1);
$splitlocation->add_sub_Location($f);
is($f->start, 13, 'Bio::Location::Split tests');
is($f->min_start, 13);
is($f->max_start,13);
$f = Bio::Location::Simple->new(-start =>30,
-end =>90,
-strand =>1);
$splitlocation->add_sub_Location($f);
$f = Bio::Location::Simple->new(-start =>11,
-end =>22,
-strand =>1);
$splitlocation->add_sub_Location($f);
$f = Bio::Location::Simple->new(-start =>19,
-end =>20,
-strand =>1);
$splitlocation->add_sub_Location($f);
$f = Bio::Location::Fuzzy->new(-start =>"<50",
-end =>61,
-strand =>1);
is($f->start, 50);
ok(! defined $f->min_start);
is($f->max_start, 50);
is(scalar($splitlocation->each_Location()), 4);
$splitlocation->add_sub_Location($f);
# For unsorted split locations like this:
# ('join(13..30,30..90,11..22,19..20,<50..61)'),
# BioPerl will assume Start and End belongs to the
# first and last segments respectively, because sorting
# would break real cases like circular cut by origin features
is($splitlocation->end, 61);
is($splitlocation->start, 13);
is($splitlocation->sub_Location(),5);
# Minimum Start and Maximum End in unsorted sublocations can be
# achieved by asking explicitly sub_Location to sort the segments
my @increase_sort_sublocs = $splitlocation->sub_Location(1); # Forward sort by Start
my @decrease_sort_sublocs = $splitlocation->sub_Location(-1); # Reverse sort by End
is($increase_sort_sublocs[0]->min_start, 11);
is($decrease_sort_sublocs[0]->max_end, 90);
is($fuzzy->to_FTstring(), '<10..20');
$fuzzy->strand(-1);
is($fuzzy->to_FTstring(), 'complement(<10..20)');
is($simple->to_FTstring(), '10..20');
$simple->strand(-1);
is($simple->to_FTstring(), 'complement(10..20)');
is( $splitlocation->to_FTstring(),
'join(13..30,30..90,11..22,19..20,<50..61)');
# test for bug #1074
$f = Bio::Location::Simple->new(-start => 5,
-end => 12,
-strand => -1);
$splitlocation->add_sub_Location($f);
is( $splitlocation->to_FTstring(),
'join(13..30,30..90,11..22,19..20,<50..61,complement(5..12))',
'Bugfix 1074');
$splitlocation->strand(-1);
is( $splitlocation->to_FTstring(),
'complement(join(13..30,30..90,11..22,19..20,<50..61,5..12))');
$f = Bio::Location::Fuzzy->new(-start => '45.60',
-end => '75^80');
is($f->to_FTstring(), '(45.60)..(75^80)');
$f->start('20>');
is($f->to_FTstring(), '>20..(75^80)');
# test that even when end < start that length is always positive
$f = Bio::Location::Simple->new(-verbose => -1,
-start => 100,
-end => 20,
-strand => 1);
is($f->length, 81, 'Positive length');
is($f->strand,-1);
# test that can call seq_id() on a split location;
$splitlocation = Bio::Location::Split->new(-seq_id => 'mysplit1');
is($splitlocation->seq_id,'mysplit1', 'seq_id() on Bio::Location::Split');
is($splitlocation->seq_id('mysplit2'),'mysplit2');
# Test Bio::Location::Exact
ok(my $exact = Bio::Location::Simple->new(-start => 10,
-end => 20,
-strand => 1,
-seq_id => 'my1'));
isa_ok($exact, 'Bio::LocationI');
isa_ok($exact, 'Bio::RangeI');
is( $exact->start, 10, 'Bio::Location::Simple EXACT');
is( $exact->end, 20);
is( $exact->seq_id, 'my1');
is( $exact->length, 11);
is( $exact->location_type, 'EXACT');
ok ($exact = Bio::Location::Simple->new(-start => 10,
-end => 11,
-location_type => 'IN-BETWEEN',
-strand => 1,
-seq_id => 'my2'));
is($exact->start, 10, 'Bio::Location::Simple IN-BETWEEN');
is($exact->end, 11);
is($exact->seq_id, 'my2');
is($exact->length, 0);
is($exact->location_type, 'IN-BETWEEN');
eval {
$exact = Bio::Location::Simple->new(-start => 10,
-end => 12,
-location_type => 'IN-BETWEEN');
};
ok( $@, 'Testing error handling' );
# testing error when assigning 10^11 simple location into fuzzy
eval {
ok $fuzzy = Bio::Location::Fuzzy->new(-start => 10,
-end => 11,
-location_type => '^',
-strand => 1,
-seq_id => 'my2');
};
ok( $@ );
$fuzzy = Bio::Location::Fuzzy->new(-location_type => '^',
-strand => 1,
-seq_id => 'my2');
$fuzzy->start(10);
eval { $fuzzy->end(11) };
ok($@);
$fuzzy = Bio::Location::Fuzzy->new(-location_type => '^',
-strand => 1,
-seq_id =>'my2');
$fuzzy->end(11);
eval {
$fuzzy->start(10);
};
ok($@);
# testing coodinate policy modules
use_ok('Bio::Location::WidestCoordPolicy');
use_ok('Bio::Location::NarrowestCoordPolicy');
use_ok('Bio::Location::AvWithinCoordPolicy');
$f = Bio::Location::Fuzzy->new(-start => '40.60',
-end => '80.100');
is $f->start, 40, 'Default coodinate policy';
is $f->end, 100;
is $f->length, 61;
is $f->to_FTstring, '(40.60)..(80.100)';
isa_ok($f->coordinate_policy, 'Bio::Location::WidestCoordPolicy');
# this gives an odd location string; is it legal?
$f->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
is $f->start, 60, 'Narrowest coodinate policy';
is $f->end, 80;
is $f->length, 21;
is $f->to_FTstring, '(60.60)..(80.80)';
isa_ok($f->coordinate_policy, 'Bio::Location::NarrowestCoordPolicy');
# this gives an odd location string
$f->coordinate_policy(Bio::Location::AvWithinCoordPolicy->new());
is $f->start, 50, 'Average coodinate policy';
is $f->end, 90;
is $f->length, 41;
is $f->to_FTstring, '(50.60)..(80.90)';
isa_ok($f->coordinate_policy, 'Bio::Location::AvWithinCoordPolicy');
# to complete the circle
$f->coordinate_policy(Bio::Location::WidestCoordPolicy->new());
is $f->start, 40, 'Widest coodinate policy';
is $f->end, 100;
is $f->length, 61;
is $f->to_FTstring, '(40.60)..(80.100)';
isa_ok($f->coordinate_policy, 'Bio::Location::WidestCoordPolicy');
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