From 6c872943597f3664cca77abbdf56f074fc5231e6 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Tue, 31 Aug 2021 06:56:35 +0300
Subject: Fix bugs with `run_reaper` function

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

* gn3/computations/qtlreaper.py: Fix some bugs
* qtlfilesexport.py: Test out running rust-qtlreaper

  Test out the qtlreaper interface code and fix some bugs caught in the
  process.
---
 qtlfilesexport.py | 7 +++++++
 1 file changed, 7 insertions(+)

(limited to 'qtlfilesexport.py')

diff --git a/qtlfilesexport.py b/qtlfilesexport.py
index 1db4ab6..799de31 100644
--- a/qtlfilesexport.py
+++ b/qtlfilesexport.py
@@ -9,6 +9,7 @@ replacing the variables in the angled brackets with the appropriate values
 """
 from gn3.computations.slink import slink
 from gn3.db_utils import database_connector
+from gn3.computations.qtlreaper import run_reaper
 from gn3.computations.heatmap import export_trait_data
 from gn3.db.traits import retrieve_trait_data, retrieve_trait_info
 from gn3.db.genotypes import build_genotype_file, load_genotype_samples
@@ -57,5 +58,11 @@ def main():
     generate_traits_file(strains_values, trait_values, traits_filename)
     print("Generated file: {}".format(traits_filename))
 
+    main_output, permutations_output = run_reaper(
+        genotype_filename, traits_filename, separate_nperm_output=True)
+
+    print("Main output: {}, Permutation output: {}".format(
+        main_output, permutations_output))
+
 if __name__ == "__main__":
     main()
-- 
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