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.
---
 gn3/computations/qtlreaper.py | 8 +++++---
 qtlfilesexport.py             | 7 +++++++
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 9b13a55..c058e14 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -42,7 +42,7 @@ def create_output_directory(path: str):
 
 def run_reaper(
         genotype_filename: str, traits_filename: str,
-        other_options: tuple = ("--n_permutations", 1000),
+        other_options: tuple = ("--n_permutations", "1000"),
         separate_nperm_output: bool = False,
         output_dir: str = TMPDIR):
     """
@@ -70,7 +70,7 @@ def run_reaper(
     The function will raise a `subprocess.CalledProcessError` exception in case
     of any errors running the `qtlreaper` command.
     """
-    create_output_directory(output_dir)
+    create_output_directory("{}/qtlreaper".format(output_dir))
     output_filename = "{}/qtlreaper/main_output_{}.txt".format(
         output_dir, random_string(10))
     output_list = ["--main_output", output_filename]
@@ -84,7 +84,9 @@ def run_reaper(
     command_list = [
         REAPER_COMMAND, "--geno", genotype_filename,
         *other_options, # this splices the `other_options` list here
-        "--traits", traits_filename, "--main_output", output_filename]
+        "--traits", traits_filename,
+        *output_list # this splices the `output_list` list here
+    ]
 
     subprocess.run(command_list, check=True)
     return (output_filename, permu_output_filename)
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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