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modify dbNSFP, make all unavailable by default
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William McLaren committed Sep 21, 2015
1 parent 516dc7f commit c1dfeab
Showing 1 changed file with 85 additions and 81 deletions.
166 changes: 85 additions & 81 deletions plugin_config.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -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 <a rel="external" href="https://drive.google.com/file/d/0B60wROKy6OqcSFNBbWVjNWl5UjQ/view?usp=sharing">dbNSFP README</a>',
# "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",
Expand Down Expand Up @@ -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",
],
},
]
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
},
Expand All @@ -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",
Expand All @@ -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",
},
Expand Down Expand Up @@ -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",
Expand Down

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