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annotate segmentation_sequenza.R @ 6:88e03bac1e36 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
author artbio
date Sun, 07 Mar 2021 12:01:21 +0000
parents e299c477b475
children e66b91475343
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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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1 # load packages that are provided in the conda env
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88e03bac1e36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
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2 # options(show.error.messages = F,
88e03bac1e36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
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3 # error = function() {
88e03bac1e36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
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4 # cat(geterrmessage(), file = stderr()); q("no", 1, F)})
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5
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(sequenza)
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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8 library(BiocParallel)
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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9 library(tidyverse)
6
88e03bac1e36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
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10 Sys.setenv(TZ = "Etc/UTC") # turnaround the tidyverse bug "In OlsonNames() : no Olson database found"
88e03bac1e36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
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11 tzdirs <- c(Sys.getenv("TZDIR"), file.path(R.home("share"),
88e03bac1e36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
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12 "zoneinfo"), "/usr/share/zoneinfo", "/usr/share/lib/zoneinfo",
88e03bac1e36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
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13 "/usr/lib/zoneinfo", "/usr/local/etc/zoneinfo", "/etc/zoneinfo",
88e03bac1e36 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit ccbc1fc0e1af1e9cf5000fe2a3f60655cd5793eb"
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14 "/usr/etc/zoneinfo")
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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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15 option_list <- list(
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16 make_option(
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17 c("-i", "--input"),
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18 default = NA,
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19 type = "character",
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20 help = "Path to Sequenza seqz processed segments file"
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21 ),
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22 make_option(
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23 c("-O", "--output_dir"),
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24 default = NA,
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25 type = "character",
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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26 help = "Output directory"
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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27 ),
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28 make_option(
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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29 c("-s", "--sample_name"),
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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30 default = NA,
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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31 type = "character",
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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32 help = "Sample name"
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33 )
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34 )
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36 opt <- parse_args(OptionParser(option_list = option_list),
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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37 args = commandArgs(trailingOnly = TRUE))
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38
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39 data_file <- opt$input
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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40 output_dir <- opt$output_dir
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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41 sample_name <- opt$sample_name
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44 ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22
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45 message(sprintf("\nExtraction step for %s", data_file))
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4
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47 chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
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48 "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
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49 "chr18", "chr19", "chr20", "chr21", "chr22")
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0
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51 segfile <- sequenza.extract(data_file,
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52 verbose = TRUE,
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53 chromosome.list = chrom_list)
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55 ## Estimation of cellularity and ploidy
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57 segfile_cp <- sequenza.fit(segfile)
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58 message(sprintf("\nEstimation step for %s\n", data_file))
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60 ## writing files and plots using default parameters
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61 message(sprintf("\nWriting files and plots for %s\n", data_file))
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63 sequenza.results(sequenza.extract = segfile,
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64 cp.table = segfile_cp,
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65 sample.id = sample_name,
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66 out.dir = output_dir)
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67 message(sprintf("\nOutput written to %s\n", output_dir))