comparison snpEffExtract.R @ 2:dc51db22310c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"

1:e362b3143cde

suppressPackageStartupMessages(library(VariantAnnotation))
suppressPackageStartupMessages(library(tidyverse))

tsv_eff_from_vcf <- function(input_vcf, output_tab) {
    read_vcf <- readVcf(input_vcf)  # nolint
    chrom_pos <- data.frame(read_vcf@rowRanges)[, c("seqnames", "start")]
    ref_alt_filter <- read_vcf@fixed[, c("REF", "ALT", "FILTER")]
    dp_af <- read_vcf@info[c("DP", "AF")]

    ## Unwrap the DNAStringList

2:dc51db22310c

suppressPackageStartupMessages(library(VariantAnnotation))
suppressPackageStartupMessages(library(tidyverse))

tsv_eff_from_vcf <- function(input_vcf, output_tab) {
    read_vcf <- readVcf(input_vcf)  # nolint
    if (!nrow(read_vcf@fixed)) {
        # no variants in file -> just write a valid header line
        write(c("CHROM", "POS", "REF", "ALT", "AF", "EFF[*].GENE", "EFF[*].EFFECT"),
              ncolumns = 7, file = output_tab, sep = "\t")
        return()
    }
    chrom_pos <- data.frame(read_vcf@rowRanges)[, c("seqnames", "start")]
    ref_alt_filter <- read_vcf@fixed[, c("REF", "ALT", "FILTER")]
    dp_af <- read_vcf@info[c("DP", "AF")]

    ## Unwrap the DNAStringList