Mercurial > repos > artbio > snvtocnv
diff sequenza_to_hrdtools_input.R @ 0:b77d7a0a45e8 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
author | artbio |
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date | Sun, 07 Mar 2021 23:19:59 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sequenza_to_hrdtools_input.R Sun Mar 07 23:19:59 2021 +0000 @@ -0,0 +1,67 @@ +options(show.error.messages = F, error = function() { + cat(geterrmessage(), file = stderr()); q("no", 1, F) }) + +# load packages that are provided in the conda env + +library(optparse) +library(tidyverse) + +option_list <- list( + make_option( + c("-i", "--input"), + default = NA, + type = "character", + help = "Path to Sequenza output segments file" + ), + make_option( + c("-o", "--output"), + default = NA, + type = "character", + help = "output file, to be used as input for HRDetect" + ), + make_option( + c("-s", "--solutions"), + default = NA, + type = "character", + help = "Path to Sequenza list of alternative solutions" + ) +) + +opt <- parse_args(OptionParser(option_list = option_list), + args = commandArgs(trailingOnly = TRUE)) + +sequenza_data <- as_tibble(read.delim(opt$input, header = TRUE)) +solutions_data <- as_tibble(read.delim(opt$solutions, header = TRUE)) + + +ploidy <- round(solutions_data$ploidy[1]) +cellularity <- solutions_data$cellularity[1] + +reformatted <- sequenza_data %>% + select( + chr = chromosome, + start = start.pos, + end = end.pos, + copynumber = CNt, + A, B + ) %>% + mutate( + ploidy = ploidy, + cellularity = cellularity, + lohtype = case_when( + copynumber == 0 ~ "HOMD", + B == 0 & A == ploidy ~ "NLOH", + B == 0 & A < ploidy & A > 0 ~ "DLOH", + copynumber > ploidy & A > B ~ "ASCNA", + copynumber > ploidy & A == B ~ "BCNA", + TRUE ~ "HET" + ) + ) + +message("Preview of output:") +print(reformatted) + +reformatted %>% + write.table(opt$output, quote = F, row.names = F, sep = "\t") + +message(sprintf("Output written to %s", opt$output))