Merge branch 'master' of https://github.com/Ensembl/ensembl

PULL_REQUEST_TEMPLATE.md

+## Requirements
+
+- Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
+- Review the [contributing guidelines](https://github.com/Ensembl/ensembl/blob/release/90/CONTRIBUTING.md#why-could-my-pull-request-be-rejected) for this repository; remember in particular:
+    - do not modify code without testing for regression
+    - provide simple unit tests to test the changes
+    - if you change the schema you must patch the test databases as well, see [Updating the schema](https://github.com/Ensembl/ensembl/blob/release/90/CONTRIBUTING.md#updating-the-schema)
+    - the PR must not fail unit testing
+
+## Description
+
+_One or more sentences describing in detail the proposed changes._
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Ut feugiat ligula vel enim congue, nec faucibus turpis ornare. Integer nulla massa, fermentum nec elit a, dapibus luctus ante. Vestibulum eleifend enim et consectetur convallis.
+
+## Use case
+
+_Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place._
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas lobortis aliquet risus id dapibus. In vulputate porta justo. Vestibulum in arcu varius, laoreet urna a, egestas dui.
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Etiam ultrices egestas urna, vel mollis felis viverra iaculis. Phasellus ac nisi imperdiet ipsum viverra porta.
+
+## Benefits
+
+_If applicable, describe the advantages the changes will have._
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean eget diam quis leo faucibus sagittis. Sed dapibus, magna ut porttitor malesuada, lorem purus tincidunt magna, ut dignissim mi quam et elit.
+
+## Possible Drawbacks
+
+_If applicable, describe any possible undesirable consequence of the changes._
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras molestie tincidunt quam, id dapibus mauris consequat eu. Phasellus in neque quis purus laoreet malesuada in sit amet tellus.
+
+## Testing
+
+_Have you added/modified unit tests to test the changes?_
+
+Yes.
+
+_If so, do the tests pass/fail?_
+
+Pass, of course.
+
+_Have you run the entire test suite and no regression was detected?_
+
+Yes.

modules/Bio/EnsEMBL/Mapper.pm

@@ -320,7 +320,12 @@ sub map_coordinates {
     my $self_coord   = $pair->{$from};
     my $target_coord = $pair->{$to};
 
-    
+    # if we haven't even reached the start, move on
+    if ( $self_coord->{'end'} < $orig_start ) { next;}
+
+    # if we have over run, break
+    if ( $self_coord->{'start'} > $end ) { last;}
+
     #
     # But not the case for haplotypes!! need to test for this case???
     # so removing this till a better solution is found
@@ -340,12 +345,6 @@ sub map_coordinates {
       $last_target_coord = $target_coord->{'id'};
     }
 
-    # if we haven't even reached the start, move on
-    if ( $self_coord->{'end'} < $orig_start ) { next;}
-
-    # if we have over run, break
-    if ( $self_coord->{'start'} > $end ) { last;}
-
     if ( $start < $self_coord->{'start'} ) {
       # gap detected
       my $gap = Bio::EnsEMBL::Mapper::Gap->new( $start, $self_coord->{'start'} - 1, $rank );

modules/Bio/EnsEMBL/ProteinFeature.pm

@@ -207,10 +207,13 @@ sub summary_as_hash {
   my %summary;
   $summary{'type'} = $self->analysis->db;
   $summary{'id'} = $self->display_id;
-  $summary{'start'} = $self->start,
-  $summary{'end'} = $self->end,
+  $summary{'start'} = $self->start;
+  $summary{'end'} = $self->end;
   $summary{'interpro'} = $self->interpro_ac;
   $summary{'description'} = $self->idesc;
+  $summary{'hit_start'} = $self->hstart;
+  $summary{'hit_end'} = $self->hend;
+  
   return \%summary;
 }
 

modules/t/proteinFeature.t

@@ -47,7 +47,9 @@ my $ilabel = 'interpro label';
 my $interpro_ac = 'interpro accession';
 my $translation_id = 1234;
 
-my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
+my $analysis_db = 'test_db';
+
+my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test', -DB => $analysis_db);
 
 
 my $f = Bio::EnsEMBL::ProteinFeature->new
@@ -94,6 +96,17 @@ ok($f->interpro_ac eq $interpro_ac);
 # check that the strand is 0
 ok($f->strand == 0);
 
+# Test summary_as_hash
+my $summary = $f->summary_as_hash();
+ok($summary->{'type'} = $analysis_db);
+ok($summary->{'id'} = $hseqname);
+ok($summary->{'start'} = $start);
+ok($summary->{'end'} = $end);
+ok($summary->{'interpro'} = $interpro_ac);
+ok($summary->{'description'} = $idesc);
+ok($summary->{'hit_start'} = $hstart);
+ok($summary->{'hit_end'} = $hend);
+
 #
 # Test setters
 #

modules/t/proteinFeatureAdaptor.t

@@ -40,7 +40,7 @@ my $pfs = $pfa->fetch_all_by_translation_id(21724);
 
 print_features($pfs);
 
-is(@$pfs, 15, "Found 15 features");
+ok(@$pfs == 15);
 
 sub print_features {
   my $features = shift;
@@ -68,7 +68,9 @@ my $hdes = "Hit description";
 my $idesc = 'interpro description';
 my $interpro_ac = 'interpro accession';
 
-my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
+my $analysis_db = 'test_db';
+
+my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test', -DB => $analysis_db);
 $multi->save('core', 'protein_feature', 'meta_coord');
 
 
@@ -88,6 +90,17 @@ my $f = Bio::EnsEMBL::ProteinFeature->new
    -IDESC       => $idesc,
    -INTERPRO_AC => $interpro_ac);
    
+
+my $summary = $f->summary_as_hash();
+is($summary->{'type'}, $analysis_db);
+is($summary->{'id'}, $hseqname);
+is($summary->{'start'}, $start);
+is($summary->{'end'}, $end);
+is($summary->{'interpro'}, $interpro_ac);
+is($summary->{'description'}, $idesc);
+is($summary->{'hit_start'}, $hstart);
+is($summary->{'hit_end'}, $hend);   
+   
 my $dbID = $pfa->store($f,21724);
 
 ok($dbID, "New object created has dbID");
@@ -106,13 +119,13 @@ is($f_by_dbID->hend, $hend);
 is($f_by_dbID->hseqname, $hseqname);
 is($f_by_dbID->hdescription, $hdes);
 is($f_by_dbID->score, $score);
-is(sprintf("%.6f", $f_by_dbID->percent_id), sprintf("%.6f", $percent_id), "Correct percent_id");
-is(sprintf("%.6f", $f_by_dbID->p_value), sprintf("%.6f", $p_value), "Correct p_value");
+is($f_by_dbID->percent_id, $percent_id);
+is($f_by_dbID->p_value, $p_value);
 
 
 $pfs = $pfa->fetch_all_by_translation_id(21724);
 
-is(@$pfs, 16, "Found 16 features");
+ok(@$pfs == 16);
 
 my @pfs = grep{$_->hdescription() eq $hdes} @$pfs;
 

travisci/trigger-dependent-build.sh

@@ -55,7 +55,9 @@ fi
 
 # The list of downstream dependent repos
 dep_repos=("Ensembl%2Fensembl%2Dcompara"
+	   "Ensembl%2Fensembl%2Dvariation"
 	   "Ensembl%2Fensembl%2Dfuncgen"
+	   "Ensembl%2Fensembl%2Dvep"
 	   "Ensembl%2Fensembl%2Drest")
 
 for dep_repo in "${dep_repos[@]}"; do