From c1dfeab2cdc58dbdaa9b1bd9bf28affb9615af24 Mon Sep 17 00:00:00 2001 From: William McLaren Date: Mon, 21 Sep 2015 15:34:08 +0100 Subject: [PATCH] modify dbNSFP, make all unavailable by default --- plugin_config.txt | 166 ++++++++++++++++++++++++---------------------- 1 file changed, 85 insertions(+), 81 deletions(-) diff --git a/plugin_config.txt b/plugin_config.txt index 672b2281..affe2d5a 100644 --- a/plugin_config.txt +++ b/plugin_config.txt @@ -30,46 +30,46 @@ my $VEP_PLUGIN_CONFIG = { { "name" => "dbNSFP_fields", "label" => "Fields to include", - "helptip" => "A comma-separated list of fields to fetch from dbNSFP; start typing to see available fields", + "helptip" => "Fields to fetch from dbNSFP; hold down the Ctrl (Windows) / Command (Mac) button to select multiple options", "value" => "", - "type" => "string", - "class" => "autocomplete-multi", + 'type' => 'dropdown', + 'multiple' => 1, + 'style' => 'height:150px', + 'required' => 1, + 'notes' => 'Field descriptions in dbNSFP README', + # "class" => "jquery-multiselect", "values" => [ - "chr", - "pos(1-based)", - "ref", - "alt", - "aaref", - "aaalt", - "rs_dbSNP142", - "hg19_chr", - "hg19_pos(1-based)", - "hg18_chr", - "hg18_pos(1-based)", - "genename", - "cds_strand", - "refcodon", - "codonpos", - "codon_degeneracy", - "Ancestral_allele", - "AltaiNeandertal", - "Denisova", - "Ensembl_geneid", - "Ensembl_transcriptid", - "Ensembl_proteinid", - "aapos", - "SIFT_score", - "SIFT_converted_rankscore", - "SIFT_pred", - "Uniprot_acc_Polyphen2", - "Uniprot_id_Polyphen2", - "Uniprot_aapos_Polyphen2", - "Polyphen2_HDIV_score", - "Polyphen2_HDIV_rankscore", - "Polyphen2_HDIV_pred", - "Polyphen2_HVAR_score", - "Polyphen2_HVAR_rankscore", - "Polyphen2_HVAR_pred", + # "chr", + # "pos(1-based)", + # "ref", + # "alt", + # "aaref", + # "aaalt", + # "rs_dbSNP142", + # "hg19_chr", + # "hg19_pos(1-based)", + # "hg18_chr", + # "hg18_pos(1-based)", + # "genename", + # "cds_strand", + # "refcodon", + # "codonpos", + # "Ensembl_geneid", + # "Ensembl_transcriptid", + # "Ensembl_proteinid", + # "aapos", + # "SIFT_score", + # "SIFT_converted_rankscore", + # "SIFT_pred", + # "Uniprot_acc_Polyphen2", + # "Uniprot_id_Polyphen2", + # "Uniprot_aapos_Polyphen2", + # "Polyphen2_HDIV_score", + # "Polyphen2_HDIV_rankscore", + # "Polyphen2_HDIV_pred", + # "Polyphen2_HVAR_score", + # "Polyphen2_HVAR_rankscore", + # "Polyphen2_HVAR_pred", "LRT_score", "LRT_converted_rankscore", "LRT_pred", @@ -114,46 +114,50 @@ my $VEP_PLUGIN_CONFIG = { "SiPhy_29way_pi", "SiPhy_29way_logOdds", "SiPhy_29way_logOdds_rankscore", - "1000Gp3_AC", - "1000Gp3_AF", - "1000Gp3_AFR_AC", - "1000Gp3_AFR_AF", - "1000Gp3_EUR_AC", - "1000Gp3_EUR_AF", - "1000Gp3_AMR_AC", - "1000Gp3_AMR_AF", - "1000Gp3_EAS_AC", - "1000Gp3_EAS_AF", - "1000Gp3_SAS_AC", - "1000Gp3_SAS_AF", + # "1000Gp3_AC", + # "1000Gp3_AF", + # "1000Gp3_AFR_AC", + # "1000Gp3_AFR_AF", + # "1000Gp3_EUR_AC", + # "1000Gp3_EUR_AF", + # "1000Gp3_AMR_AC", + # "1000Gp3_AMR_AF", + # "1000Gp3_EAS_AC", + # "1000Gp3_EAS_AF", + # "1000Gp3_SAS_AC", + # "1000Gp3_SAS_AF", "TWINSUK_AC", "TWINSUK_AF", "ALSPAC_AC", "ALSPAC_AF", - "ESP6500_AA_AC", - "ESP6500_AA_AF", - "ESP6500_EA_AC", - "ESP6500_EA_AF", - "ExAC_AC", - "ExAC_AF", - "ExAC_Adj_AC", - "ExAC_Adj_AF", - "ExAC_AFR_AC", - "ExAC_AFR_AF", - "ExAC_AMR_AC", - "ExAC_AMR_AF", - "ExAC_EAS_AC", - "ExAC_EAS_AF", - "ExAC_FIN_AC", - "ExAC_FIN_AF", - "ExAC_NFE_AC", - "ExAC_NFE_AF", - "ExAC_SAS_AC", - "ExAC_SAS_AF", + # "ESP6500_AA_AC", + # "ESP6500_AA_AF", + # "ESP6500_EA_AC", + # "ESP6500_EA_AF", + # "ExAC_AC", + # "ExAC_AF", + # "ExAC_Adj_AC", + # "ExAC_Adj_AF", + # "ExAC_AFR_AC", + # "ExAC_AFR_AF", + # "ExAC_AMR_AC", + # "ExAC_AMR_AF", + # "ExAC_EAS_AC", + # "ExAC_EAS_AF", + # "ExAC_FIN_AC", + # "ExAC_FIN_AF", + # "ExAC_NFE_AC", + # "ExAC_NFE_AF", + # "ExAC_SAS_AC", + # "ExAC_SAS_AF", "clinvar_rs", "clinvar_clnsig", "clinvar_trait", - "Interpro_domain" + # "Interpro_domain", + "codon_degeneracy", + "Ancestral_allele", + "AltaiNeandertal", + "Denisova", ], }, ] @@ -329,7 +333,7 @@ my $VEP_PLUGIN_CONFIG = { "key" => "GeneSplicer", "label" => "GeneSplicer", "helptip" => "Detects splice sites in genomic DNA", - "available" => 1, + "available" => 0, "enabled" => 0, "section" => "Splicing predictions", "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/GeneSplicer.pm", @@ -349,7 +353,7 @@ my $VEP_PLUGIN_CONFIG = { "key" => "MaxEntScan", "label" => "MaxEntScan", "helptip" => "Sequence motif and maximum entropy based splice site consensus predictions", - "available" => 1, + "available" => 0, "enabled" => 0, "section" => "Splicing predictions", "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/MaxEntScan.pm", @@ -371,7 +375,7 @@ my $VEP_PLUGIN_CONFIG = { "key" => "Blosum62", "label" => "BLOSUM62", "helptip" => "BLOSUM62 amino acid conservation score", - "available" => 1, + "available" => 0, "enabled" => 0, "section" => "Conservation", "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Blosum62.pm", @@ -393,7 +397,7 @@ my $VEP_PLUGIN_CONFIG = { { "key" => "Conservation", "helptip" => "Retrieves a conservation score from the Ensembl Compara databases for variant positions", - "available" => 1, + "available" => 0, "enabled" => 0, "section" => "Conservation", "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Conservation.pm", @@ -431,7 +435,7 @@ my $VEP_PLUGIN_CONFIG = { { "key" => "CSN", "helptip" => "Reports Clinical Sequencing Nomenclature (CSN) for variants", - "available" => 1, + "available" => 0, "enabled" => 0, "section" => "Identifiers", "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/CSN.pm", @@ -442,7 +446,7 @@ my $VEP_PLUGIN_CONFIG = { "key" => "HGVSshift", "label" => "Unshifted HGVS", "helptip" => "By default VEP 3' shifts HGVS notations in repetetive sequence; use this plugin to additionally report unshifted notations", - "available" => 1, + "available" => 0, "enabled" => 0, "section" => "Identifiers", "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/HGVSshift.pm", @@ -479,7 +483,7 @@ my $VEP_PLUGIN_CONFIG = { "key" => "miRNA", "label" => "miRNA structure", "helptip" => "Determines where in the secondary structure of a miRNA a variant falls", - "available" => 1, + "available" => 0, "enabled" => 0, "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/miRNA.pm", }, @@ -491,7 +495,7 @@ my $VEP_PLUGIN_CONFIG = { { "key" => "UpDownDistance", "label" => "Upstream/Downstream distance", - "available" => 1, + "available" => 0, "enabled" => 0, "helptip" => "Change the distance to transcript (default is 5000bp) for which VEP assigns upstream and downstream consequences", "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/UpDownDistance.pm", @@ -513,7 +517,7 @@ my $VEP_PLUGIN_CONFIG = { "key" => "NearestGene", "label" => "Nearest gene", "helptip" => "Finds the nearest gene to non-genic variants", - "available" => 1, + "available" => 0, "enabled" => 0, "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/NearestGene.pm", }, @@ -590,7 +594,7 @@ my $VEP_PLUGIN_CONFIG = { "key" => "GO", "label" => "Gene Ontology", "helptip" => "Retrieves Gene Ontology terms associated with transcripts/translations via the Ensembl API", - "available" => 1, + "available" => 0, "enabled" => 0, "plugin_url" => "https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/GO.pm", "section" => "Gene data",