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| author | Muriithi Frederick Muriuki | 2021-08-31 06:51:18 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-31 06:55:10 +0300 |
| commit | 6ab866183aeac8553fdcda9217e4445da2b4836b (patch) | |
| tree | a94e70179af04b5cffe04b27f27b29e69c104997 /gn3/settings.py | |
| parent | b8777bcfee70325263d5389367e3a93ec2842f69 (diff) | |
| download | genenetwork3-6ab866183aeac8553fdcda9217e4445da2b4836b.tar.gz | |
Provide utilities for genotype files
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.
Diffstat (limited to 'gn3/settings.py')
| -rw-r--r-- | gn3/settings.py | 4 |
1 files changed, 4 insertions, 0 deletions
diff --git a/gn3/settings.py b/gn3/settings.py index d137370..a08f846 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -27,3 +27,7 @@ BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R" # qtlreaper command REAPER_COMMAND = "{}/bin/qtlreaper".format(os.environ.get("GUIX_ENVIRONMENT")) + +# genotype files +GENOTYPE_FILES = os.environ.get( + "GENOTYPE_FILES", "{}/genotype_files/genotype".format(os.environ.get("HOME"))) |