From fb5615db4f93b97bf34aed73a97a1d20f92a744f Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 3 Feb 2023 12:07:13 +0100
Subject: [PATCH] add seed arg for DNAcopy (#101)

* add seed arg for DNAcopy
* lint code with black
---
 wisecondorX/include/CBS.R    | 4 ++++
 wisecondorX/main.py          | 3 +++
 wisecondorX/predict_tools.py | 1 +
 3 files changed, 8 insertions(+)
 mode change 100755 => 100644 wisecondorX/main.py

diff --git a/wisecondorX/include/CBS.R b/wisecondorX/include/CBS.R
index 6f4de52..fe25cf9 100644
--- a/wisecondorX/include/CBS.R
+++ b/wisecondorX/include/CBS.R
@@ -21,6 +21,7 @@ suppressMessages(library("jsonlite"))
 input <- read_json(in.file)
 ratio <- as.numeric(unlist(input$results_r))
 weights <- as.numeric(unlist(input$results_w))
+seed <- as.numeric(input$seed)
 gender <- input$ref_gender
 alpha <- as.numeric(input$alpha)
 binsize <- as.numeric(input$binsize)
@@ -63,6 +64,9 @@ for.cbs <- for.cbs[cbs.mask,]
 
 # CBS
 
+if (is.na(seed) || seed == '') {
+  set.seed(seed)
+}
 CNA.object <- CNA(for.cbs$y, for.cbs$chromosome, for.cbs$x, data.type = "logratio", sampleid = "X")
 f = file()
 sink(file=f) ## silence output
diff --git a/wisecondorX/main.py b/wisecondorX/main.py
old mode 100755
new mode 100644
index 6a1d3b9..c34f988
--- a/wisecondorX/main.py
+++ b/wisecondorX/main.py
@@ -474,6 +474,9 @@ def main():
         action="store_true",
         help="Add the output name as plot title",
     )
+    parser_test.add_argument(
+        "--seed", type=int, default=None, help="Seed for segmentation algorithm"
+    )
     parser_test.set_defaults(func=tool_test)
 
     args = parser.parse_args(sys.argv[1:])
diff --git a/wisecondorX/predict_tools.py b/wisecondorX/predict_tools.py
index 91a0548..5b57afe 100644
--- a/wisecondorX/predict_tools.py
+++ b/wisecondorX/predict_tools.py
@@ -247,6 +247,7 @@ def exec_cbs(rem_input, results):
         "ref_gender": str(rem_input["ref_gender"]),
         "alpha": str(rem_input["args"].alpha),
         "binsize": str(rem_input["binsize"]),
+        "seed": str(rem_input["args"].seed),
         "results_r": results["results_r"],
         "results_w": results["results_w"],
         "infile": str("{}_01.json".format(json_cbs_dir)),