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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 /gn3/computations | |
| 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 'gn3/computations')
| -rw-r--r-- | gn3/computations/qtlreaper.py | 2 |
1 files changed, 1 insertions, 1 deletions
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])] + [ |