Merge pull request #1336 from olaaustine/update_pick_mane_changes

Ensembl · Jan 18, 2023 · c894a81 · c894a81
2 parents 6270b19 + f50d4a6
commit c894a81
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Showing 2 changed files with 15 additions and 12 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Config.pm b/modules/Bio/EnsEMBL/VEP/Config.pm
@@ -95,7 +95,7 @@ our %DEFAULTS = (
   failed            => 0,
   core_type         => 'core',
   polyphen_analysis => 'humvar',
-  pick_order        => [qw(mane canonical appris tsl biotype ccds rank length ensembl refseq )],
+  pick_order        => [qw(mane_select mane_plus_clinical canonical appris tsl biotype ccds rank length ensembl refseq )],
   terminal_width    => 48,
   vcf_info_field    => 'CSQ',
   ucsc_data_root    => 'http://hgdownload.cse.ucsc.edu/goldenpath/',
@@ -370,7 +370,7 @@ our %VALID = (
   terms           => [qw(SO display NCBI)],
   sift            => [qw(s p b)],
   polyphen        => [qw(s p b)],
-  pick_order      => [qw(mane canonical appris tsl biotype ccds rank length ensembl refseq)],
+  pick_order      => [qw(mane_select mane_plus_clinical canonical appris tsl biotype ccds rank length ensembl refseq)],
   nearest         => [qw(transcript gene symbol)],
   compress_output => [qw(gzip bgzip)],
 );

diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory.pm
@@ -671,14 +671,15 @@ sub filter_StructuralVariationOverlapAlleles {
   Example    : $picked = $of->pick_worst_VariationFeatureOverlapAllele($vfoas);
   Description: Selects one VariationFeatureOverlapAllele from a list using criteria
                defined in the param pick_order. Criteria are in this default order:
-                1: mane
-                2: canonical
-                3: transcript support level
-                4: biotype (protein coding favoured)
-                5: consequence rank
-                6: transcript length
-                7: transcript from Ensembl?
-                8: transcript from RefSeq?
+                1: MANE_Select 
+                2: MANE_Plus_Clinical
+                3: canonical
+                4: transcript support level
+                5: biotype (protein coding favoured)
+                6: consequence rank
+                7: transcript length
+                8: transcript from Ensembl?
+                9: transcript from RefSeq?
   Returntype : Bio::EnsEMBL::Variation::VariationFeatureOverlapAllele
   Exceptions : none
   Caller     : filter_VariationFeatureOverlapAlleles(),
@@ -704,7 +705,8 @@ sub pick_worst_VariationFeatureOverlapAllele {
 
       # these will only be used by transcript types, default to 1 for others
       # to avoid writing an else clause below
-      mane => 1,
+      mane_select => 1,
+      mane_plus_clinical => 1,
       canonical => 1,
       ccds => 1,
       length => 0,
@@ -719,7 +721,8 @@ sub pick_worst_VariationFeatureOverlapAllele {
       my $tr = $vfoa->feature;
 
       # 0 is "best"
-      $info->{mane} = scalar(grep {$_->code eq 'MANE_Select'}  @{$tr->get_all_Attributes()}) ? 0 : 1;
+      $info->{mane_select} = scalar(grep {$_->code eq 'MANE_Select'}  @{$tr->get_all_Attributes()}) ? 0 : 1;
+      $info->{mane_plus_clinical} = scalar(grep {$_->code eq 'MANE_Plus_Clinical'}  @{$tr->get_all_Attributes()}) ? 0 : 1;
       $info->{canonical} = $tr->is_canonical ? 0 : 1;
       $info->{biotype} = $tr->biotype eq 'protein_coding' ? 0 : 1;
       $info->{ccds} = $tr->{_ccds} && $tr->{_ccds} ne '-' ? 0 : 1;