Mercurial > repos > artbio > snvtocnv

comparison segmentation_sequenza.R @ 8:67213c4eefa6 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
author artbio
date Sun, 07 Mar 2021 23:13:08 +0000
parents e66b91475343
children f3bacfd9b670
comparison
equal deleted inserted replaced
7:e66b91475343 8:67213c4eefa6
1 options(warn = -1) 1 options(show.error.messages = F, error = function() {
2 cat(geterrmessage(), file = stderr()); q("no", 1, F) })
2 3
3 # load packages that are provided in the conda env 4 # load packages that are provided in the conda env
4 library(optparse) 5 library(optparse)
5 library(sequenza) 6 library(sequenza)
6 library(BiocParallel) 7 library(BiocParallel)
7 library(tidyverse) 8 library(tidyverse)
9 library(readr)
10
8 option_list <- list( 11 option_list <- list(
9 make_option( 12 make_option(
10 c("-i", "--input"), 13 c("-i", "--input"),
11 default = NA, 14 default = NA,
12 type = "character", 15 type = "character",
39 42
40 chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", 43 chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
41 "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", 44 "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
42 "chr18", "chr19", "chr20", "chr21", "chr22") 45 "chr18", "chr19", "chr20", "chr21", "chr22")
43 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
44 segfile <- sequenza.extract(data_file, 53 segfile <- sequenza.extract(data_file,
45 verbose = TRUE, 54 verbose = FALSE,
46 chromosome.list = chrom_list) 55 chromosome.list = chrom_list)
47 56
48 ## Estimation of cellularity and ploidy 57 ## Estimation of cellularity and ploidy
49 58
50 segfile_cp <- sequenza.fit(segfile) 59 segfile_cp <- sequenza.fit(segfile)