diff options
Diffstat (limited to 'gn2/wqflask/marker_regression')
| -rw-r--r-- | gn2/wqflask/marker_regression/run_mapping.py | 26 |
1 files changed, 18 insertions, 8 deletions
diff --git a/gn2/wqflask/marker_regression/run_mapping.py b/gn2/wqflask/marker_regression/run_mapping.py index 7d2d40f7..92bbe321 100644 --- a/gn2/wqflask/marker_regression/run_mapping.py +++ b/gn2/wqflask/marker_regression/run_mapping.py @@ -25,7 +25,7 @@ Redis = Redis() from flask import Flask, g -from gn2.base.trait import GeneralTrait +from gn2.base.trait import GeneralTrait, create_trait from gn2.base import data_set from gn2.base import species from gn2.base import webqtlConfig @@ -49,7 +49,7 @@ class RunMapping: # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py) self.temp_uuid = temp_uuid - # ZS: Needed to zoom in or remap temp traits like PCA traits + # Needed to zoom in or remap temp traits like PCA traits if "temp_trait" in start_vars and start_vars['temp_trait'] != "False": self.temp_trait = "True" self.group = self.dataset.group.name @@ -60,7 +60,7 @@ class RunMapping: self.json_data = {} self.json_data['lodnames'] = ['lod.hk'] - # ZS: Sometimes a group may have a genofile that only includes a subset of samples + # Sometimes a group may have a genofile that only includes a subset of samples genofile_samplelist = [] if 'genofile' in start_vars: if start_vars['genofile'] != "": @@ -95,10 +95,6 @@ class RunMapping: else: self.n_samples = len([val for val in self.vals if val != "x"]) - # ZS: Check if genotypes exist in the DB in order to create links for markers - - self.geno_db_exists = geno_db_exists(self.dataset) - self.mapping_method = start_vars['method'] if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] @@ -138,6 +134,7 @@ class RunMapping: self.bootstrap_results = [] self.covariates = start_vars['covariates'] if "covariates" in start_vars else "" self.categorical_vars = [] + self.geno_db_exists = False # ZS: This is passed to GN1 code for single chr mapping self.selected_chr = -1 @@ -310,6 +307,9 @@ class RunMapping: if len(results) == 0: self.no_results = True else: + # Check if genotypes exist in the DB in order to create links for markers + self.geno_db_exists = geno_db_exists(self.dataset, results[0]['name']) + if self.pair_scan == True: self.figure_data = results[0] self.table_data = results[1] @@ -656,11 +656,21 @@ def write_input_for_browser(this_dataset, gwas_results, annotations): return [gwas_filename, annot_filename] -def geno_db_exists(this_dataset): +def geno_db_exists(this_dataset, first_marker): + """ + Check if genotypes are databased + + This checks two things: + - A genotypes dataset exists for this group + - The first marker in the genotype file is in the genotypes dataset, + since there might be a mismatch between the file and databased markers + """ geno_db_name = this_dataset.group.name + "Geno" try: geno_db = data_set.create_dataset( dataset_name=geno_db_name, get_samplelist=False) + geno_trait = create_trait(name=first_marker, dataset_name=geno_db_name) + return "True" except: return "False" |