Implement module for interfacing with rust-qtlreaper

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

* gn3/computations/heatmap.py: move `generate_traits_file` function to new
  module
* gn3/computations/qtlreaper.py: new module to interface with the
  `rust-qtlreaper` utility.
* gn3/settings.py: Provide setting for the path to the `rust-qtlreaper`
  utility
* qtlfilesexport.py: Move `random_string` function to new module. Update to
  use functions in new module.

  Provide a module with functions to be used to interface with
  `rust-qtlreaper`. This module essentially contains all the functions that
  are needed to build the files needed for, and to run the qtlreaper utility.

1 files changed, 1 insertions, 9 deletions

diff --git a/qtlfilesexport.py b/qtlfilesexport.py
index 2e7c9c2..0543dc9 100644
--- a/qtlfilesexport.py
+++ b/qtlfilesexport.py
@@ -7,16 +7,14 @@ Run with:
 
 replacing the variables in the angled brackets with the appropriate values
 """
-import random
-import string
 from gn3.computations.slink import slink
 from gn3.db_utils import database_connector
 from gn3.computations.heatmap import export_trait_data
 from gn3.db.traits import retrieve_trait_data, retrieve_trait_info
+from gn3.computations.qtlreaper import random_string, generate_traits_file
 from gn3.computations.heatmap import (
     cluster_traits,
     compute_heatmap_order,
-    generate_traits_file,
     retrieve_strains_and_values)
 
 TMPDIR = "tmp/qtltests"
@@ -35,11 +33,6 @@ def trait_fullnames():
         "UCLA_BXDBXH_CARTILAGE_V2::ILM4200064",
         "UCLA_BXDBXH_CARTILAGE_V2::ILM3140463"]
 
-def random_string(length):
-    return "".join(
-        random.choices(
-            string.ascii_letters + string.digits, k=length))
-
 def main():
     """entrypoint function"""
     conn = database_connector()[0]
@@ -56,7 +49,6 @@ def main():
     strains_and_values = retrieve_strains_and_values(
         orders, strains, exported_traits_data_list)
     strains_values = strains_and_values[0][1]
-    strains_values2 = strains_and_values[1][1]
     trait_values = [t[2] for t in strains_and_values]
     traits_filename = "{}/traits_test_file_{}.txt".format(
         TMPDIR, random_string(10))