cre.panel_filter.R

###############################################################################
# Filter a csv report with variants having Ensembl_gene_id field against
# a gene panel csv having ensembl_gene_id field
###############################################################################
# variant_report.csv is the output of cre has Ensembl_gene_id, 
# panel.csv = gene panel with ensembl_gene_id column
filter_variants <- function(variant_report.csv, panel.csv, output.csv){
    variants <- read.csv(variant_report.csv, stringsAsFactors = F)    
    panel <- read.csv(panel.csv, stringsAsFactors = F)
    variants.panel <- variants[variants$Ensembl_gene_id %in% panel$ensembl_gene_id,]
    write.csv(variants.panel, output.csv, row.names = F)
}

# when the panel is from genomics England
# https://panelapp.genomicsengland.co.uk/panels/60/
# panel should be avaliable in panel_name.tsv in the current directory
# panel_name = "Primary immunodeficiency"
#panel_name = "Periodic fever syndromes"
# Periodic fever syndromes
filter_variants_genomics_england_panel <- function(variant_report.csv, panel.tsv, output.csv){
    variants <- read.csv(variant_report.csv, stringsAsFactors = F)
    panel <- read.delim(panel.tsv, stringsAsFactors = F)

    panel <- panel[,c("Gene.Symbol","Model_Of_Inheritance","Phenotypes","UserRatings_Green_amber_red","EnsemblId.GRch37.")]

    colnames(panel) <- c("PanelAPP.Gene.Symbol", "PanelAPP.Model_Of_Inheritance",
                         "PanelAPP.Phenotypes", "PanelAPP.UserRatings_Green_amber_red", 
                         "PanelAPP.EnsemblId.GRch37")

    variants.ens <- variants[variants$Ensembl_gene_id %in% panel$PanelAPP.EnsemblId.GRch37,]
    variants.gene <- variants[variants$Gene %in% panel$PanelAPP.Gene.Symbol,]
    
    variants <- unique(rbind(variants.ens,variants.gene))
    write.csv(variants, output.csv, row.names = F)
}

args = commandArgs(trailingOnly = T)

if (is.null(args[4])){
    filter_variants(args[1], args[2], args[3])
}else{
    filter_variants_genomics_england_panel(args[1], args[2], args[3])
}