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-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py5
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py4
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html1
3 files changed, 8 insertions, 2 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 96a91452..f23c390e 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -70,8 +70,9 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
this_dataset.group.name,
gwa_output_filename)
else:
- gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/GWA.json' % (flat_files('genotype/bimbam'),
- this_dataset.group.name)
+ gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ gwa_output_filename)
else:
gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('genotype/bimbam'),
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 93d75a03..687cfeb5 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -257,6 +257,10 @@ class MarkerRegression(object):
self.controlLocus = ""
if 'covariates' in start_vars.keys():
self.covariates = start_vars['covariates']
+ if 'maf' in start_vars.keys():
+ self.maf = start_vars['maf']
+ if 'use_loco' in start_vars.keys():
+ self.use_loco = start_vars['use_loco']
#try:
self.selectedChr = int(start_vars['selected_chr'])
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index c6c6bc23..5c457275 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -20,6 +20,7 @@
<input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
{% endfor %}
<input type="hidden" name="maf">
+ <input type="hidden" name="use_loco" value="{{ use_loco }}">
<input type="hidden" name="selected_chr" value="{{ selectedChr }}">
<input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
<input type="hidden" name="num_perm" value="{{ nperm }}">