Commit 7976b564 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

more tests for untested methods

parent 5fb74911
......@@ -75,26 +75,6 @@ my $seq2 = $contig->seq();
ok($seq1 eq $seq2);
#
# 12-13 fetch_by_fpc_name
#
#my $fpc_name = 'NT_011387';
#$slice = $slice_adaptor->fetch_by_supercontig_name($fpc_name);
#ok($new_slice->chr_start);
#ok($new_slice->chr_end);
#
# 14 - 15 fetch_by_clone_accession
#
#my $clone_acc = 'AL031658';
#$slice = $slice_adaptor->fetch_by_clone_accession($clone_acc);
#$new_slice = $slice_adaptor->fetch_by_clone_accession($clone_acc, $FLANKING);
#ok($new_slice->chr_start == $slice->chr_start - $FLANKING);
#ok($new_slice->chr_end == $slice->chr_end + $FLANKING);
#
# 16-17 fetch by transcript_stable_id
#
......@@ -107,6 +87,17 @@ ok($new_slice->start == $slice->start - $FLANKING);
ok($new_slice->end == $slice->end + $FLANKING);
#
# fetch_by_exon_stable_id
#
my $e_stable_id = 'ENSE00001048794';
$slice = $slice_adaptor->fetch_by_exon_stable_id($e_stable_id);
$new_slice = $slice_adaptor->fetch_by_exon_stable_id($e_stable_id, $FLANKING);
ok($new_slice->start == $slice->start - $FLANKING);
ok($new_slice->end == $slice->end + $FLANKING);
#
# 18-19 fetch by transcript_id
#
......@@ -320,8 +311,10 @@ ok($updated_slice->seq_region_length() == $chr_len);
ok($updated_slice->seq_region_name eq $name);
#
# Store an assembly between the slices
# Retrieve and remove said assembly
#
my $asm_start = 9999;
my $asm_slice = $chr_slice->sub_Slice( $asm_start, $asm_start + $ctg_len - 1 );
......@@ -330,6 +323,14 @@ my $str = $slice_adaptor->store_assembly( $asm_slice, $ctg_slice );
ok( $str eq "chromosome:NCBI33:testregion2:9999:10048:1<>".
"contig::testregion:1:50:1" );
my $new_mapper = $slice_adaptor->fetch_assembly($asm_slice, $ctg_slice);
is($new_mapper->from->name, 'chromosome:NCBI33:testregion2:9999:10048:1', 'Mapping from chromosome');
is($new_mapper->to->name, 'contig::testregion:1:50:1', 'Mapping to contig');
$slice_adaptor->remove_assembly($asm_slice, $ctg_slice);
my $empty_mapper = $slice_adaptor->fetch_assembly($asm_slice, $ctg_slice);
is($empty_mapper, undef, 'Mapper has been removed');
my $ctg_map = $chr_slice->project( $ctg_cs->name, $ctg_cs->version );
# Test currently fails as assembly cached somewhere.
#ok( @$ctg_map == 1 and
......@@ -661,6 +662,26 @@ ok(!defined $slice_adaptor->fetch_by_toplevel_location('1:-100--50', 1), 'Checki
ok(!defined $strand, 'Strand is undefined');
}
## Test patch data
my $patch_db = $multi->get_DBAdaptor('patch');
$slice_adaptor = $patch_db->get_SliceAdaptor();
my $unique_slices = $slice_adaptor->fetch_by_region_unique("chromosome", "HG1304_PATCH");
my $unique_slice = $unique_slices->[0];
my $initial_slice = $slice_adaptor->fetch_by_region("chromosome", "HG1304_PATCH");
my $exceptions = $initial_slice->get_all_AssemblyExceptionFeatures();
is($unique_slice->start, $exceptions->[0]->start, "Start of patch");
is($unique_slice->end, $exceptions->[0]->end, "End of patch");
## Test karyotype data
my $band_slice = $slice_adaptor->fetch_by_chr_band('6', 'p21.33');
is($band_slice->seq_region_name, '6', 'Fetched chromosome 6');
############# METHODS BELOW HERE
sub test_toplevel_location {
......
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