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| author | zsloan | 2017-09-22 16:05:58 +0000 |
|---|---|---|
| committer | zsloan | 2017-09-22 16:05:58 +0000 |
| commit | 6c0e665d86c501b4a1640e067d46ecb61a3ae1bf (patch) | |
| tree | cf5e69a4b54d5846431562a4b4f04d8ebe60e24f | |
| parent | 90b267ce7d399c3c198c57e0e76e81e95fb41691 (diff) | |
| download | genenetwork2-6c0e665d86c501b4a1640e067d46ecb61a3ae1bf.tar.gz | |
Fixed issue that caused LOCO to not work when remapping or using single chromosome view
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 1 |
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 }}"> |