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| author | Muriithi Frederick Muriuki | 2021-08-30 11:44:37 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-30 11:44:37 +0300 |
| commit | 58f59b8f7df82969b58a604070aec095d17e0501 (patch) | |
| tree | a428d08e0a5eefe8d608fe74fc04f30f3952c362 /README.md | |
| parent | bb1fd69fa24cec4ff605450d241601b3f0ced8cb (diff) | |
| download | genenetwork3-58f59b8f7df82969b58a604070aec095d17e0501.tar.gz | |
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.
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 4 |
1 files changed, 3 insertions, 1 deletions
@@ -136,8 +136,10 @@ Under the **"Trait"** column, the traits are numbered from **T1** to **T<n>** 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. |