Mercurial > repos > artbio > snvtocnv
comparison 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 |
|---|---|
| date | Sun, 07 Mar 2021 23:19:59 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:b77d7a0a45e8 |
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| 1 options(show.error.messages = F, error = function() { | |
| 2 cat(geterrmessage(), file = stderr()); q("no", 1, F) }) | |
| 3 | |
| 4 # load packages that are provided in the conda env | |
| 5 | |
| 6 library(optparse) | |
| 7 library(tidyverse) | |
| 8 | |
| 9 option_list <- list( | |
| 10 make_option( | |
| 11 c("-i", "--input"), | |
| 12 default = NA, | |
| 13 type = "character", | |
| 14 help = "Path to Sequenza output segments file" | |
| 15 ), | |
| 16 make_option( | |
| 17 c("-o", "--output"), | |
| 18 default = NA, | |
| 19 type = "character", | |
| 20 help = "output file, to be used as input for HRDetect" | |
| 21 ), | |
| 22 make_option( | |
| 23 c("-s", "--solutions"), | |
| 24 default = NA, | |
| 25 type = "character", | |
| 26 help = "Path to Sequenza list of alternative solutions" | |
| 27 ) | |
| 28 ) | |
| 29 | |
| 30 opt <- parse_args(OptionParser(option_list = option_list), | |
| 31 args = commandArgs(trailingOnly = TRUE)) | |
| 32 | |
| 33 sequenza_data <- as_tibble(read.delim(opt$input, header = TRUE)) | |
| 34 solutions_data <- as_tibble(read.delim(opt$solutions, header = TRUE)) | |
| 35 | |
| 36 | |
| 37 ploidy <- round(solutions_data$ploidy[1]) | |
| 38 cellularity <- solutions_data$cellularity[1] | |
| 39 | |
| 40 reformatted <- sequenza_data %>% | |
| 41 select( | |
| 42 chr = chromosome, | |
| 43 start = start.pos, | |
| 44 end = end.pos, | |
| 45 copynumber = CNt, | |
| 46 A, B | |
| 47 ) %>% | |
| 48 mutate( | |
| 49 ploidy = ploidy, | |
| 50 cellularity = cellularity, | |
| 51 lohtype = case_when( | |
| 52 copynumber == 0 ~ "HOMD", | |
| 53 B == 0 & A == ploidy ~ "NLOH", | |
| 54 B == 0 & A < ploidy & A > 0 ~ "DLOH", | |
| 55 copynumber > ploidy & A > B ~ "ASCNA", | |
| 56 copynumber > ploidy & A == B ~ "BCNA", | |
| 57 TRUE ~ "HET" | |
| 58 ) | |
| 59 ) | |
| 60 | |
| 61 message("Preview of output:") | |
| 62 print(reformatted) | |
| 63 | |
| 64 reformatted %>% | |
| 65 write.table(opt$output, quote = F, row.names = F, sep = "\t") | |
| 66 | |
| 67 message(sprintf("Output written to %s", opt$output)) |