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, 0 insertions, 8 deletions

diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index 3e96ed2..dcd64b1 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -230,11 +230,3 @@ 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)