From 1a3901b174d00af8fa7f5ae78b810de66024b5ab Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Fri, 27 Aug 2021 15:49:53 +0300
Subject: Export trait data to file

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* Provide a function to export the given strains and traits data into a traits
  file for use with `rust-qtlreaper`.
---
 gn3/computations/heatmap.py | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'gn3')

diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index da13ceb..2f92048 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -229,3 +229,11 @@ def retrieve_strains_and_values(orders, strainlist, traits_data_list):
         values = []
 
     return rets
+
+def generate_traits_file(strains, trait_values, traits_filename):
+    header = "Traits\t{}\n".format("\t".join(strains))
+    data = [header] + [
+        "T{}\t{}\n".format(i+1, "\t".join([str(i) for i in t]))
+        for i,t in enumerate(trait_values)]
+    with open(traits_filename, "w") as outfile:
+        outfile.writelines(data)
-- 
cgit v1.2.3