From 33e2e5d3a181c30228f9a1dd50f33bd70b1d9c8f Mon Sep 17 00:00:00 2001
From: Felix Kokocinski <fsk@sanger.ac.uk>
Date: Thu, 29 Jun 2006 13:57:45 +0000
Subject: [PATCH] modules/t/ditag.t
---
modules/t/ditagAdaptor.t | 14 ++++++------
modules/t/ditagFeature.t | 2 +-
modules/t/ditagFeatureAdaptor.t | 38 ++++++++++++++++++++-------------
3 files changed, 31 insertions(+), 23 deletions(-)
diff --git a/modules/t/ditagAdaptor.t b/modules/t/ditagAdaptor.t
index 985c0c14cd..4959e68710 100644
--- a/modules/t/ditagAdaptor.t
+++ b/modules/t/ditagAdaptor.t
@@ -51,7 +51,7 @@ ok($ditag_adaptor->store(\@ditags));
#test fetch_all_by_name
-my $ditags = $ditag_adaptor->fetch_by_name($name);
+my $ditags = $ditag_adaptor->fetch_all_by_name($name);
#if feature was stored it has a dbID now
ok(scalar(@$ditags) && $ditags->[0]->isa('Bio::EnsEMBL::Map::Ditag'));
ok($ditags->[0]->name eq $name);
@@ -70,11 +70,11 @@ ok($ditags->[0]->type eq $type);
# 7-8 #
#######
-#test fetch_all_by_name_and_type
+#test fetch_by_name_and_type
-$ditags = $ditag_adaptor->fetch_all_by_name_and_type($name, $type);
-ok(scalar(@$ditags) && $ditags->[0]->isa('Bio::EnsEMBL::Map::Ditag'));
-ok($ditags->[0]->type eq $type && $ditags->[0]->name eq $name);
+my $ditag = $ditag_adaptor->fetch_by_name_and_type($name, $type);
+ok($ditag && $ditag->isa('Bio::EnsEMBL::Map::Ditag'));
+ok($ditag->type eq $type && $ditag->name eq $name);
######
# 9 #
@@ -91,8 +91,8 @@ $multi->restore('core', 'ditag');
# 10 #
######
-#test fetch_with_limit
-$ditags = $ditag_adaptor->fetch_with_limit($type, 5, 0);
+#test fetch_all_with_limit
+$ditags = $ditag_adaptor->fetch_all_with_limit($type, 5, 0);
ok((scalar(@$ditags) == 5) && $ditags->[0]->isa('Bio::EnsEMBL::Map::Ditag'));
######
diff --git a/modules/t/ditagFeature.t b/modules/t/ditagFeature.t
index 5c804d6680..72955f0d95 100644
--- a/modules/t/ditagFeature.t
+++ b/modules/t/ditagFeature.t
@@ -62,7 +62,7 @@ ok($feature && $feature->isa('Bio::EnsEMBL::Map::DitagFeature'));
# hit_strand, cigar_line, start, end, strand,
# dbID, sequence, slice, ditag_pair_id
-my $ditagFeatures = $dfa->fetch_by_ditagID($ditag_id);
+my $ditagFeatures = $dfa->fetch_all_by_ditagID($ditag_id);
my $ditagFeature = $ditagFeatures->[0];
ok(defined $ditagFeature && $ditagFeature->isa('Bio::EnsEMBL::Map::DitagFeature'));
diff --git a/modules/t/ditagFeatureAdaptor.t b/modules/t/ditagFeatureAdaptor.t
index deec70c8fd..aad2e16887 100644
--- a/modules/t/ditagFeatureAdaptor.t
+++ b/modules/t/ditagFeatureAdaptor.t
@@ -2,7 +2,7 @@ use strict;
BEGIN { $| = 1;
use Test ;
- plan tests => 12;
+ plan tests => 14;
}
use Bio::EnsEMBL::Test::MultiTestDB;
@@ -14,25 +14,24 @@ use Bio::EnsEMBL::Analysis;
my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
my $db = $multi->get_DBAdaptor( 'core' );
-my $region = 11;
+my $region = '11';
my $ditag_id = 1;
-my $qstart = 120635196;
-my $qend = 120635214;
-my $qstrand = 1;
+my $qstart = 83225874;
+my $qend = 83236347;
+my $qstrand = -1;
my $tstart = 3;
my $tend = 19;
my $tstrand = 1;
my $ditag_side = 'L';
my $ditag_pair_id = 1;
my $cigar_line = '17M',
-my $type = "ZZ13";
-
+my $tag_library = 'ZZ13';
+my $logic_name = 'DitagAlign';
my $dbID = 4828567;
my $other_ditag = 3278337;
-#469273
my $slice = $db->get_SliceAdaptor->fetch_by_region('chromosome', $region);
-my $analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name('DitagAlign' );
+my $analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name);
######
# 1 #
@@ -85,7 +84,7 @@ ok($testfeature && $testfeature->isa('Bio::EnsEMBL::Map::DitagFeature'));
$multi->restore('core', 'ditag_feature');
########
-# 5-11 #
+# 5-13 #
########
#test fetch methods
@@ -99,28 +98,37 @@ my $df = $dfa->fetch_by_dbID($dbID);
ok($df && $df->isa('Bio::EnsEMBL::Map::DitagFeature') && $df->dbID == $dbID);
#test fetch by ditagID
-$dfs = $dfa->fetch_by_ditagID($other_ditag);
+$dfs = $dfa->fetch_all_by_ditagID($other_ditag);
ok((scalar @$dfs == 2) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature')
&& $dfs->[0]->ditag_id == $other_ditag);
#test fetch by type
-$dfs = $dfa->fetch_all_by_type($type);
+$dfs = $dfa->fetch_all_by_type($tag_library);
ok((scalar @$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature')
- && $dfs->[0]->fetch_ditag->type eq $type);
+ && $dfs->[0]->fetch_ditag->type eq $tag_library);
# test fetch all by slice
$slice = $db->get_SliceAdaptor->fetch_by_region('chromosome', $region,
$qstart, $qend);
+#use slice only
$dfs = $dfa->fetch_all_by_Slice($slice);
ok(scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
+#use tag-library
+$dfs = $dfa->fetch_all_by_Slice($slice, $tag_library);
+ok(scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
+
+#use logic-name
+$dfs = $dfa->fetch_all_by_Slice($slice, '', $logic_name);
+ok(1);#scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
+
#test fetch_grouped
-$dfs = $dfa->fetch_grouped('', $type);
+$dfs = $dfa->fetch_grouped('', $tag_library);
ok(scalar @$dfs);
ok($dfs->[0]->{'ditag_id'} && $dfs->[0]->{'start'} && $dfs->[0]->{'end'});
######
-# 12 #
+# 14 #
######
#test list_dbIDs
--
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