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annotate segmentation_sequenza.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 f3bacfd9b670
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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0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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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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5 library(optparse)
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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6 library(sequenza)
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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7 library(BiocParallel)
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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8 library(tidyverse)
8
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9 library(readr)
67213c4eefa6 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
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11 option_list <- list(
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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12 make_option(
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13 c("-i", "--input"),
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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14 default = NA,
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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15 type = "character",
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16 help = "Path to Sequenza seqz processed segments file"
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17 ),
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18 make_option(
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19 c("-O", "--output_dir"),
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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20 default = NA,
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21 type = "character",
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22 help = "Output directory"
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23 ),
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24 make_option(
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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25 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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26 default = NA,
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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27 type = "character",
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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28 help = "Sample name"
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29 )
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30 )
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32 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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33 args = commandArgs(trailingOnly = TRUE))
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35 data_file <- opt$input
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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36 output_dir <- opt$output_dir
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37 sample_name <- opt$sample_name
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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40 ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22
0e54da14f831 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"
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41 message(sprintf("\nExtraction step for %s", data_file))
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f3bacfd9b670 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
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43 chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
f3bacfd9b670 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
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44 "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
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45 "chr18", "chr19", "chr20", "chr21", "chr22", "chrX")
2
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47 Sys.setenv(TZDIR = "/usr/share/zoneinfo/")
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48 Sys.setenv(TZ = "US/Eastern")
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49 options(tz = "US/Eastern")
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50 Sys.timezone(location = TRUE)
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0
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53 segfile <- sequenza.extract(data_file,
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54 verbose = FALSE,
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55 chromosome.list = chrom_list)
0
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57 ## Estimation of cellularity and ploidy
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59 segfile_cp <- sequenza.fit(segfile)
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60 message(sprintf("\nEstimation step for %s\n", data_file))
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62 ## writing files and plots using default parameters
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63 message(sprintf("\nWriting files and plots for %s\n", data_file))
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65 sequenza.results(sequenza.extract = segfile,
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66 cp.table = segfile_cp,
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67 sample.id = sample_name,
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68 out.dir = output_dir)
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69 message(sprintf("\nOutput written to %s\n", output_dir))