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| author | zsloan | 2022-06-01 20:43:00 +0000 |
|---|---|---|
| committer | zsloan | 2022-06-01 20:43:00 +0000 |
| commit | cba418b1953c36558f0bb05da98165d52cbfb52b (patch) | |
| tree | 37b110e42a76005043f744aa1425c9485cb6caaa | |
| parent | 508a24488190ee5ca22294fd4331d857efcf170b (diff) | |
| download | genenetwork2-cba418b1953c36558f0bb05da98165d52cbfb52b.tar.gz | |
Fix the way R/qtl is called in the GN2 REST API
| -rw-r--r-- | wqflask/wqflask/api/mapping.py | 18 |
1 files changed, 8 insertions, 10 deletions
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index f8b0d8bd..d1cc368e 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -52,17 +52,15 @@ def do_mapping_for_api(start_vars): elif mapping_params['mapping_method'] == "rqtl": header_row = ["name", "chr", "cM", "lod_score"] if mapping_params['num_perm'] > 0: - _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], - mapping_params['perm_check'], mapping_params[ - 'num_perm'], - mapping_params['do_control'], mapping_params[ - 'control_marker'], - mapping_params['manhattan_plot'], mapping_params['pair_scan']) + _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl(this_trait.name, vals, samples, dataset, None, "Mb", mapping_params['rqtl_model'], + mapping_params['rqtl_method'], mapping_params['num_perm'], None, + mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['manhattan_plot'], None) else: - result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'], - mapping_params['perm_check'], mapping_params['num_perm'], - mapping_params['do_control'], mapping_params['control_marker'], - mapping_params['manhattan_plot'], mapping_params['pair_scan']) + result_markers = rqtl_mapping.run_rqtl(this_trait.name, vals, samples, dataset, None, "Mb", mapping_params['rqtl_model'], + mapping_params['rqtl_method'], mapping_params['num_perm'], None, + mapping_params['do_control'], mapping_params['control_marker'], + mapping_params['manhattan_plot'], None) if mapping_params['limit_to']: result_markers = result_markers[:mapping_params['limit_to']] |