Fix linting errors, minor bugs and reorganise code

* Fix some linting errors and some minor bugs caught by the linter.
  Move the `random_string` function to separate module for use in multiple
  places in the code.

2 files changed, 18 insertions, 16 deletions

diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index 92014cf..1143450 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -6,6 +6,7 @@ generate various kinds of heatmaps.
 from functools import reduce
 from typing import Any, Dict, Sequence
 from gn3.computations.slink import slink
+from gn3.computations.qtlreaper import generate_traits_file
 from gn3.computations.correlations2 import compute_correlation
 from gn3.db.genotypes import build_genotype_file, load_genotype_samples
 from gn3.db.traits import (
@@ -155,14 +156,14 @@ def heatmap_data(traits_names, conn: Any):
         for fullname in traits_names]
     traits_list = tuple(x[0] for x in traits_details)
     traits_data_list = [x[1] for x in traits_details]
-    exported_traits_data_list = tuple(
-        export_trait_data(td, strainlist) for td in traits_data_list)
     genotype_filename = build_genotype_file(traits_list[0]["riset"])
     strainlist = load_genotype_samples(genotype_filename)
+    exported_traits_data_list = tuple(
+        export_trait_data(td, strainlist) for td in traits_data_list)
     slink_data = slink(cluster_traits(exported_traits_data_list))
     ordering_data = compute_heatmap_order(slink_data)
     strains_and_values = retrieve_strains_and_values(
-        orders, strainlist, exported_traits_data_list)
+        ordering_data, strainlist, exported_traits_data_list)
     strains_values = strains_and_values[0][1]
     trait_values = [t[2] for t in strains_and_values]
     traits_filename = generate_traits_filename()
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 3b8e4db..30c7051 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -3,17 +3,10 @@ This module contains functions to interact with the `qtlreaper` utility for
 computation of QTLs.
 """
 import os
-import random
-import string
 import subprocess
+from gn3.random import random_string
 from gn3.settings import TMPDIR, REAPER_COMMAND
 
-def random_string(length):
-    """Generate a random string of length `length`."""
-    return "".join(
-        random.choices(
-            string.ascii_letters + string.digits, k=length))
-
 def generate_traits_file(strains, trait_values, traits_filename):
     """
     Generate a traits file for use with `qtlreaper`.
@@ -25,11 +18,13 @@ def generate_traits_file(strains, trait_values, traits_filename):
         computation of QTLs.
     """
     header = "Trait\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[:-1])] + [
-        "T{}\t{}".format(len(trait_values), "\t".join([str(i) for i in t]))
-        for t in trait_values[-1:]]
+    data = (
+        [header] +
+        ["T{}\t{}\n".format(i+1, "\t".join([str(i) for i in t]))
+         for i, t in enumerate(trait_values[:-1])] +
+        ["T{}\t{}".format(
+            len(trait_values), "\t".join([str(i) for i in t]))
+         for t in trait_values[-1:]])
     with open(traits_filename, "w") as outfile:
         outfile.writelines(data)
 
@@ -93,6 +88,9 @@ def run_reaper(
 
 
 def parse_reaper_main_results(results_file):
+    """
+    Parse the results file of running QTLReaper into a list of dicts.
+    """
     with open(results_file, "r") as infile:
         lines = infile.readlines()
 
@@ -104,6 +102,9 @@ def parse_reaper_main_results(results_file):
     return [dict(zip(header, __parse_line(line))) for line in lines[1:]]
 
 def parse_reaper_permutation_results(results_file):
+    """
+    Parse the results QTLReaper permutations into a list of values.
+    """
     with open(results_file, "r") as infile:
         lines = infile.readlines()