From 58f59b8f7df82969b58a604070aec095d17e0501 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 30 Aug 2021 11:44:37 +0300
Subject: Fix issues with traits file format

* README.md: update header: Traits ==> Trait
* gn3/computations/qtlreaper.py: update header: Traits ==> Trait
* qtlfilesexport.py: Choose only BXD strains

  Rename the first column header from "Traits" to "Trait" to correspond with
  what `rust-qtlreaper` expects.

  Choose only the BXD strains for the proof-of-concept example - this helped
  bring out the fact that the traits file SHOULD NOT contain a strain column
  for a strain that does not exist in the genotype file in consideration.

  If the traits file has a strain column which does not exist in the genotype
  file, then `rust-qtlreaper` fails with a panic, since, from what I can tell,
  it tries to get a value from the genotype file for the non-existent strain,
  which results to a `None` type. Subsequent attempts at running an operation
  on the `None` type lead to the panic.
---
 gn3/computations/qtlreaper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index a88659e..9b13a55 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -24,7 +24,7 @@ def generate_traits_file(strains, trait_values, traits_filename):
     traits_filename: The tab-separated value to put the values in for
         computation of QTLs.
     """
-    header = "Traits\t{}\n".format("\t".join(strains))
+    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])] + [
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