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-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py5
1 files changed, 1 insertions, 4 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 16e639dc..61e4897c 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -46,7 +46,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
genofile_name,
TEMPDIR,
k_output_filename)
- logger.debug("k_command:" + generate_k_command)
+
os.system(generate_k_command)
gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
@@ -78,7 +78,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
TEMPDIR,
k_output_filename)
- logger.debug("k_command:" + generate_k_command)
os.system(generate_k_command)
gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
@@ -94,8 +93,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
else:
gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename)
-
- logger.debug("gemma_command:" + gemma_command)
os.system(gemma_command)
else:
gwa_output_filename = output_files