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annotate sequenza_to_hrdtools_input.R @ 10:0a19b63c521d draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 116f2555558a283190cd1dd60ee25b359bcda51e
author artbio
date Fri, 20 May 2022 17:07:09 +0000
parents 67213c4eefa6
children
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67213c4eefa6 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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1 options(show.error.messages = F, error = function() {
67213c4eefa6 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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2 cat(geterrmessage(), file = stderr()); q("no", 1, F) })
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e66b91475343 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 7df896b940e80984168b1fa6326c4d862e7e208c"
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4 # load packages that are provided in the conda env
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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6 library(optparse)
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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7 library(tidyverse)
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9 option_list <- list(
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10 make_option(
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11 c("-i", "--input"),
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12 default = NA,
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13 type = "character",
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14 help = "Path to Sequenza output segments file"
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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15 ),
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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16 make_option(
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17 c("-o", "--output"),
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18 default = NA,
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19 type = "character",
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20 help = "output file, to be used as input for HRDetect"
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21 ),
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22 make_option(
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23 c("-s", "--solutions"),
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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24 default = NA,
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25 type = "character",
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26 help = "Path to Sequenza list of alternative solutions"
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27 )
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28 )
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30 opt <- parse_args(OptionParser(option_list = option_list),
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31 args = commandArgs(trailingOnly = TRUE))
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33 sequenza_data <- as_tibble(read.delim(opt$input, header = TRUE))
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34 solutions_data <- as_tibble(read.delim(opt$solutions, header = TRUE))
0
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37 ploidy <- round(solutions_data$ploidy[1])
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38 cellularity <- solutions_data$cellularity[1]
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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40 reformatted <- sequenza_data %>%
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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41 select(
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42 chr = chromosome,
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43 start = start.pos,
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44 end = end.pos,
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45 copynumber = CNt,
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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46 A, B
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47 ) %>%
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48 mutate(
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49 ploidy = ploidy,
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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50 cellularity = cellularity,
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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51 lohtype = case_when(
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52 copynumber == 0 ~ "HOMD",
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53 B == 0 & A == ploidy ~ "NLOH",
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54 B == 0 & A < ploidy & A > 0 ~ "DLOH",
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55 copynumber > ploidy & A > B ~ "ASCNA",
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56 copynumber > ploidy & A == B ~ "BCNA",
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57 TRUE ~ "HET"
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58 )
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59 )
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61 message("Preview of output:")
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62 print(reformatted)
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64 reformatted %>%
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65 write.table(opt$output, quote = F, row.names = F, sep = "\t")
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67 message(sprintf("Output written to %s", opt$output))