--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentation_sequenza.R	Sun Mar 07 23:19:59 2021 +0000
@@ -0,0 +1,69 @@
+options(show.error.messages = F, error = function() {
+        cat(geterrmessage(), file = stderr()); q("no", 1, F) })
+
+# load packages that are provided in the conda env
+library(optparse)
+library(sequenza)
+library(BiocParallel)
+library(tidyverse)
+library(readr)
+
+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))
+
+chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
+               "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
+               "chr18", "chr19", "chr20", "chr21", "chr22")
+
+Sys.setenv(TZDIR = "/usr/share/zoneinfo/")
+Sys.setenv(TZ = "US/Eastern")
+options(tz = "US/Eastern")
+Sys.timezone(location = TRUE)
+
+
+segfile <- sequenza.extract(data_file,
+                            verbose = FALSE,
+                            chromosome.list = chrom_list)
+
+## 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))