Merge pull request #1734 from likhitha-surapaneni/improve_gencode_pri…

…mary Improving --gencode_primary and --flag_gencode_primary
Ensembl · Aug 8, 2024 · e06699f · e06699f
2 parents 9ffc8fd + 822d90c
commit e06699f
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Showing 2 changed files with 16 additions and 1 deletion.
diff --git a/modules/Bio/EnsEMBL/VEP/Config.pm b/modules/Bio/EnsEMBL/VEP/Config.pm
@@ -606,6 +606,7 @@ our %INCOMPATIBLE = (
   af_gnomade    => [qw(af_gnomad)],
   quiet       => [qw(verbose)],
   refseq      => [qw(gencode_basic merged)],
+  gencode_primary => [qw(gencode_basic refseq)],
   json        => [qw(vcf tab)],
   vcf         => [qw(json tab)],
   tab         => [qw(vcf json)],
@@ -704,6 +705,20 @@ sub new {
     $config->{cache} = 1;
   }
 
+   # throw a warning for GENCODE basic if assembly is not GRCh38
+  if (defined($config->{'gencode_basic'}) && $config->{'gencode_basic'} && defined($config->{'assembly'}) && lc($config->{'assembly'}) ne 'grch38') {
+    printf("WARNING: --gencode_basic option is currently only available for human on the GRCh38 assembly\n");
+  }
+
+  # throw a warning for GENCODE primary if assembly is not GRCh38
+  if (defined($config->{'gencode_primary'}) && $config->{'gencode_primary'} && defined($config->{'assembly'}) && lc($config->{'assembly'}) ne 'grch38') {
+    printf("WARNING: --gencode_primary option is currently only available for human on the GRCh38 assembly\n");
+  }
+
+    # throw a warning for GENCODE primary if assembly is not GRCh38
+  if (defined($config->{'flag_gencode_primary'}) && $config->{'flag_gencode_primary'} && defined($config->{'assembly'}) && lc($config->{'assembly'}) ne 'grch38') {
+    printf("WARNING: --flag_gencode_primary option is currently only available for human on the GRCh38 assembly\n");
+  }
   my $config_command = "";
 
   my @skip_opts = qw(web_output host port stats_file user warning_file input_data);

diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -259,7 +259,7 @@ our %FIELD_DESCRIPTIONS = (
   'CHECK_REF'	       => 'Reports variants where the input reference does not match the expected reference',
   'UPLOADED_ALLELE'    => 'The variant allele uploaded',
   'SHIFT_LENGTH'       => 'Reports the number of bases the insertion or deletion has been shifted relative to the underlying transcript due to right alignment before consequence calculation',
-  'GENCODE_PRIMARY'    => 'Reports if transcript is Gencode Primary'
+  'GENCODE_PRIMARY'    => 'Reports if transcript is GENCODE primary'
 );
 
 our @DEFAULT_OUTPUT_COLS = qw(