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.

1 files changed, 7 insertions, 0 deletions

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()