diff options
Diffstat (limited to 'gn3/computations/qtlreaper.py')
| -rw-r--r-- | gn3/computations/qtlreaper.py | 5 |
1 files changed, 3 insertions, 2 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index 981a9c8..8c970f2 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -7,7 +7,7 @@ import subprocess from typing import Union from gn3.chancy import random_string -from gn3.settings import TMPDIR, REAPER_COMMAND +from gn3.settings import TMPDIR def generate_traits_file(samples, trait_values, traits_filename): """ @@ -39,6 +39,7 @@ def create_output_directory(path: str): pass def run_reaper( + reaper_cmd: str, genotype_filename: str, traits_filename: str, other_options: tuple = ("--n_permutations", "1000"), separate_nperm_output: bool = False, @@ -81,7 +82,7 @@ def run_reaper( permu_output_filename = None command_list = [ - REAPER_COMMAND, "--geno", genotype_filename, + reaper_cmd, "--geno", genotype_filename, *other_options, # this splices the `other_options` list here "--traits", traits_filename, *output_list # this splices the `output_list` list here |