Mercurial > repos > artbio > snvtocnv

comparison segmentation_sequenza.R @ 0:b77d7a0a45e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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 d2833cfb3f08
comparison
equal deleted inserted replaced
-1:000000000000 0:b77d7a0a45e8
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 library(optparse)
6 library(sequenza)
7 library(BiocParallel)
8 library(tidyverse)
9 library(readr)
10
11 option_list <- list(
12 make_option(
13 c("-i", "--input"),
14 default = NA,
15 type = "character",
16 help = "Path to Sequenza seqz processed segments file"
17 ),
18 make_option(
19 c("-O", "--output_dir"),
20 default = NA,
21 type = "character",
22 help = "Output directory"
23 ),
24 make_option(
25 c("-s", "--sample_name"),
26 default = NA,
27 type = "character",
28 help = "Sample name"
29 )
30 )
31
32 opt <- parse_args(OptionParser(option_list = option_list),
33 args = commandArgs(trailingOnly = TRUE))
34
35 data_file <- opt$input
36 output_dir <- opt$output_dir
37 sample_name <- opt$sample_name
38
39
40 ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22
41 message(sprintf("\nExtraction step for %s", data_file))
42
43 chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
44 "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
45 "chr18", "chr19", "chr20", "chr21", "chr22")
46
47 Sys.setenv(TZDIR = "/usr/share/zoneinfo/")
48 Sys.setenv(TZ = "US/Eastern")
49 options(tz = "US/Eastern")
50 Sys.timezone(location = TRUE)
51
52
53 segfile <- sequenza.extract(data_file,
54 verbose = FALSE,
55 chromosome.list = chrom_list)
56
57 ## Estimation of cellularity and ploidy
58
59 segfile_cp <- sequenza.fit(segfile)
60 message(sprintf("\nEstimation step for %s\n", data_file))
61
62 ## writing files and plots using default parameters
63 message(sprintf("\nWriting files and plots for %s\n", data_file))
64
65 sequenza.results(sequenza.extract = segfile,
66 cp.table = segfile_cp,
67 sample.id = sample_name,
68 out.dir = output_dir)
69 message(sprintf("\nOutput written to %s\n", output_dir))