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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/qtlreaper.py: Fix some bugs
* qtlfilesexport.py: Test out running rust-qtlreaper
Test out the qtlreaper interface code and fix some bugs caught in the
process.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: New module
* gn3/settings.py: Add new configuration variable
* qtlfilesexport.py: Test out new code
Add a module containing functions dealing with the genotype files.
Add a configuration variable to point to the location of the genotype files.
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* 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.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: move `generate_traits_file` function to new
module
* gn3/computations/qtlreaper.py: new module to interface with the
`rust-qtlreaper` utility.
* gn3/settings.py: Provide setting for the path to the `rust-qtlreaper`
utility
* qtlfilesexport.py: Move `random_string` function to new module. Update to
use functions in new module.
Provide a module with functions to be used to interface with
`rust-qtlreaper`. This module essentially contains all the functions that
are needed to build the files needed for, and to run the qtlreaper utility.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* As part of the development effort, this commit provides a proof-of-concept
as a reference for generating the traits data file.
It might be useful for verifying that the functions that are called are
working as is expected.
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