diff segmentation_sequenza.R @ 0:0e54da14f831 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentation_sequenza.R	Thu Feb 18 18:59:53 2021 +0000
@@ -0,0 +1,61 @@
+# load packages that are provided in the conda env
+options(show.error.messages = F,
+       error = function() {
+           cat(geterrmessage(), file = stderr()); q("no", 1, F)})
+Sys.setenv(TZ = "Pacific/Auckland") # turnaround the tidyverse bug "In OlsonNames() : no Olson database found"
+
+
+library(optparse)
+library(sequenza)
+library(BiocParallel)
+library(tidyverse)
+
+option_list <- list(
+  make_option(
+    c("-i", "--input"),
+    default = NA,
+    type = "character",
+    help = "Path to Sequenza seqz processed segments file"
+  ),
+  make_option(
+    c("-O", "--output_dir"),
+    default = NA,
+    type = "character",
+    help = "Output directory"
+  ),
+  make_option(
+    c("-s", "--sample_name"),
+    default = NA,
+    type = "character",
+    help = "Sample name"
+  )
+)
+
+opt <- parse_args(OptionParser(option_list = option_list),
+                 args = commandArgs(trailingOnly = TRUE))
+
+data_file <- opt$input
+output_dir <- opt$output_dir
+sample_name <- opt$sample_name
+
+
+## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22
+message(sprintf("\nExtraction step for %s", data_file))
+
+segfile <- sequenza.extract(data_file,
+                            verbose = TRUE) # ,
+                            # chromosome.list = as.character(c(1:22)))
+
+## Estimation of cellularity and ploidy
+
+segfile_cp <- sequenza.fit(segfile)
+message(sprintf("\nEstimation step for %s\n", data_file))
+
+## writing files and plots using default parameters
+message(sprintf("\nWriting files and plots for %s\n", data_file))
+
+sequenza.results(sequenza.extract = segfile,
+                 cp.table = segfile_cp,
+                 sample.id = sample_name,
+                 out.dir = output_dir)
+message(sprintf("\nOutput written to %s\n", output_dir))