diff options
| -rw-r--r-- | wqflask/wqflask/api/mapping.py | 25 |
1 files changed, 23 insertions, 2 deletions
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py index 25643b4e..42de6bb7 100644 --- a/wqflask/wqflask/api/mapping.py +++ b/wqflask/wqflask/api/mapping.py @@ -2,6 +2,7 @@ from base import data_set from base.trait import create_trait, retrieve_sample_data from wqflask.marker_regression import gemma_mapping, rqtl_mapping +from wqflask.show_trait.show_trait import normf def do_mapping_for_api(start_vars): assert('db' in start_vars) @@ -23,7 +24,8 @@ def do_mapping_for_api(start_vars): genofile_samplelist = get_genofile_samplelist(dataset) if (len(genofile_samplelist) > 0): - for sample in genofile_samplelist: + samplelist = genofile_samplelist + for sample in samplelist: in_trait_data = False for item in this_trait.data: if this_trait.data[item].name == sample: @@ -35,7 +37,8 @@ def do_mapping_for_api(start_vars): if not in_trait_data: vals.append("x") else: - for sample in dataset.group.samplelist: + samplelist = dataset.group.samplelist + for sample in samplelist: in_trait_data = False for item in this_trait.data: if this_trait.data[item].name == sample: @@ -47,6 +50,20 @@ def do_mapping_for_api(start_vars): if not in_trait_data: vals.append("x") + if mapping_params['qnorm']: + vals_minus_x = [float(val) for val in vals if val != "x"] + qnorm_vals = normf(vals_minus_x) + qnorm_vals_with_x = [] + counter = 0 + for val in vals: + if val == "x": + qnorm_vals_with_x.append("x") + else: + qnorm_vals_with_x.append(qnorm_vals[counter]) + counter += 1 + + vals = qnorm_vals_with_x + # It seems to take an empty string as default. This should probably be changed. covariates = "" @@ -148,6 +165,10 @@ def initialize_parameters(start_vars, dataset, this_trait): except: mapping_params['perm_check'] = False + mapping_params['qnorm'] = False + if 'qnorm' in start_vars: + mapping_params['qnorm'] = True + mapping_params['genofile'] = False if 'genofile' in start_vars: mapping_params['genofile'] = start_vars['genofile'] |