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authorMuriithi Frederick Muriuki2021-08-31 06:56:35 +0300
committerMuriithi Frederick Muriuki2021-08-31 06:56:35 +0300
commit6c872943597f3664cca77abbdf56f074fc5231e6 (patch)
treede5232493c2337a969ee278e11bc1f8412b98f78 /gn3
parent6ab866183aeac8553fdcda9217e4445da2b4836b (diff)
downloadgenenetwork3-6c872943597f3664cca77abbdf56f074fc5231e6.tar.gz
Fix bugs with `run_reaper` function
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.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/qtlreaper.py8
1 files changed, 5 insertions, 3 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 9b13a55..c058e14 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -42,7 +42,7 @@ def create_output_directory(path: str):
def run_reaper(
genotype_filename: str, traits_filename: str,
- other_options: tuple = ("--n_permutations", 1000),
+ other_options: tuple = ("--n_permutations", "1000"),
separate_nperm_output: bool = False,
output_dir: str = TMPDIR):
"""
@@ -70,7 +70,7 @@ def run_reaper(
The function will raise a `subprocess.CalledProcessError` exception in case
of any errors running the `qtlreaper` command.
"""
- create_output_directory(output_dir)
+ create_output_directory("{}/qtlreaper".format(output_dir))
output_filename = "{}/qtlreaper/main_output_{}.txt".format(
output_dir, random_string(10))
output_list = ["--main_output", output_filename]
@@ -84,7 +84,9 @@ def run_reaper(
command_list = [
REAPER_COMMAND, "--geno", genotype_filename,
*other_options, # this splices the `other_options` list here
- "--traits", traits_filename, "--main_output", output_filename]
+ "--traits", traits_filename,
+ *output_list # this splices the `output_list` list here
+ ]
subprocess.run(command_list, check=True)
return (output_filename, permu_output_filename)