From cf046406b3ec21b5f5d2781e5840851ae2134e31 Mon Sep 17 00:00:00 2001
From: dglemos <dlemos@ebi.ac.uk>
Date: Mon, 18 Nov 2024 14:41:53 +0000
Subject: [PATCH] Remove prints

---
 .../AnnotationSource/Database/Variation.pm    |  2 --
 modules/Bio/EnsEMBL/VEP/OutputFactory.pm      |  4 ---
 modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm |  4 ---
 .../VEP/Pipeline/DumpVEP/Dumper/Variation.pm  | 27 +++++--------------
 4 files changed, 7 insertions(+), 30 deletions(-)

diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Variation.pm b/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Variation.pm
index 099b05aef..b320de367 100644
--- a/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Variation.pm
+++ b/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Variation.pm
@@ -62,8 +62,6 @@ use Digest::MD5 qw(md5_hex);
 
 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 
-use Data::Dumper;
-
 use base qw(
   Bio::EnsEMBL::VEP::AnnotationSource::Database
   Bio::EnsEMBL::VEP::AnnotationType::Variation
diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory.pm
index c700a3ab0..5d5b3f5b6 100755
--- a/modules/Bio/EnsEMBL/VEP/OutputFactory.pm
+++ b/modules/Bio/EnsEMBL/VEP/OutputFactory.pm
@@ -1022,8 +1022,6 @@ sub add_colocated_variant_info {
   );
 
   my %clin_sigs;
-  
-  # print "***vf_existing: ", Dumper($vf->{existing});
 
   foreach my $ex(
     sort {
@@ -1044,8 +1042,6 @@ sub add_colocated_variant_info {
     # ID
     push @{$hash->{Existing_variation}}, $ex->{variation_name} if $ex->{variation_name};
 
-    # print "\nvariation name: ", $ex->{variation_name}, "\n";
-
     # Variation Synonyms
     # VEP fetches the variation synonyms from the cache
     push @{$hash->{VAR_SYNONYMS}}, $ex->{var_synonyms} if $self->{var_synonyms} && $ex->{var_synonyms} && !$self->{_config}->{_params}->{is_vr};
diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm
index 7c9cf8bd0..793babc44 100755
--- a/modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm
+++ b/modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm
@@ -90,8 +90,6 @@ use Bio::EnsEMBL::VEP::Utils qw(numberify);
 use JSON;
 use Scalar::Util qw(looks_like_number);
 
-use Data::Dumper;
-
 my %SKIP_KEYS = (
   'Uploaded_variation' => 1,
   'Location' => 1,
@@ -474,8 +472,6 @@ sub add_colocated_variant_info_JSON {
 
   push @{$hash->{colocated_variants}}, $ex;
 
-  print "-> ", Dumper($hash->{colocated_variants});
-
   return $hash;
 }
 
diff --git a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm
index 749ca1007..f26b4c8db 100644
--- a/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm
+++ b/modules/Bio/EnsEMBL/VEP/Pipeline/DumpVEP/Dumper/Variation.pm
@@ -35,8 +35,6 @@ use warnings;
 use FileHandle;
 use File::Path qw(mkpath);
 
-use Data::Dumper;
-
 use Bio::EnsEMBL::VEP::Config;
 use Bio::EnsEMBL::VEP::AnnotationSource::Database::Variation;
 use Bio::EnsEMBL::VEP::AnnotationSource::Cache::Variation;
@@ -69,20 +67,19 @@ sub run {
   my $region_size = $self->param('region_size');
 
   my $hive_dbc = $self->dbc;
-  # die "(2) ", Dumper($hive_dbc);
-  # $hive_dbc->disconnect_if_idle() if defined $hive_dbc;
-  # die "(3)";
+  $hive_dbc->disconnect_if_idle() if defined $hive_dbc;
+
   my $as = Bio::EnsEMBL::VEP::AnnotationSource::Database::Variation->new({
     config => $config,
     cache_region_size => $region_size,
   });
-  # die "(4)";
+
   my $cache = Bio::EnsEMBL::VEP::AnnotationSource::Cache::Variation->new({
     config => $config,
     cache_region_size => $region_size,
     dir => $self->get_cache_dir($vep_params)
   });
-  # die "(5)";
+
   # create prefixed names here to use later
   if($vep_params->{freq_vcf} && !$self->{freq_vcf}) {
     foreach my $vcf_conf(@{$vep_params->{freq_vcf}}) {
@@ -95,7 +92,7 @@ sub run {
     }
     $self->{freq_vcf} = $vep_params->{freq_vcf};
   }
-  # die "(6)";
+
   $self->dump_chrs($as, $cache);
 
   # bgzip and tabix-index all_vars files
@@ -226,23 +223,14 @@ sub dump_obj {
   }
 
   # get freqs from VCFs?
-  # $self->freqs_from_vcf($obj, $chr) if $self->{freq_vcf};
-  
-  open(FH, '>>', "/hps/nobackup/flicek/ensembl/variation/dlemos/vep/test_code/clin_sig_clinvar_somatic/dump_cache/log.txt") or die $!;
+  $self->freqs_from_vcf($obj, $chr) if $self->{freq_vcf};
 
   my $pubmed = $self->pubmed;
   my $var_synonyms = $self->var_synonyms;
   foreach my $v(@$obj) {
-
-    print FH "->", Dumper($v);
-
     my $tmp_clinical_impact = '';
-    my @tmp_ci;
     if($v->{clinical_impact}) {
-      foreach my $pf (@{$v->{clinical_impact}}) {
-        push @tmp_ci, $pf->{final_somatic_clin_sig};
-      }
-      $tmp_clinical_impact = join(";", @tmp_ci);
+      $tmp_clinical_impact = $v->{clinical_impact};
     }
 
     my @tmp = (
@@ -276,7 +264,6 @@ sub dump_obj {
       print $all_vars_fh "\n";
     }
   }
-  close(FH);
   close DUMP;
 }