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. --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index 0e0e509..b54015f 100644 --- a/README.md +++ b/README.md @@ -136,8 +136,10 @@ Under the **"Trait"** column, the traits are numbered from **T1** to **T** wh As an example, you could end up with a trait file like the following: ```txt -Traits BXD27 BXD32 DBA/2J BXD21 ... +Trait BXD27 BXD32 DBA/2J BXD21 ... T1 10.5735 9.27408 9.48255 9.18253 ... T2 6.4471 6.7191 5.98015 6.68051 ... ... ``` + +It is very important that the column header names for the strains correspond to the genotype file used. -- cgit v1.2.3