diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 25 |
1 files changed, 12 insertions, 13 deletions
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 290c4a14..80094057 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -104,7 +104,7 @@ class RunMapping: if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] else: - mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash]).replace("/", "_") + mapping_results_filename = "_".join([self.dataset.group.name, self.mapping_method, self.vals_hash]).replace("/", "_") self.mapping_results_path = "{}{}.csv".format( webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) @@ -405,8 +405,8 @@ class RunMapping: total_markers = len(self.qtl_results) with Bench("Exporting Results"): - export_mapping_results(self.dataset, self.this_trait, self.qtl_results, - self.mapping_results_path, self.mapping_scale, self.score_type, + export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, + self.mapping_method, self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples, self.vals_hash) with Bench("Trimming Markers for Figure"): @@ -525,7 +525,11 @@ class RunMapping: return trimmed_genotype_data -def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples, vals_hash): +def export_mapping_results(dataset, trait, markers, results_path, mapping_method, mapping_scale, score_type, transform, covariates, n_samples, vals_hash): + if mapping_scale == "physic": + scale_string = "Mb" + else: + scale_string = "cM" with open(results_path, "w+") as output_file: output_file.write( "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") @@ -535,6 +539,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Trait: " + trait.display_name + "\n") output_file.write("Trait Hash: " + vals_hash + "\n") output_file.write("N Samples: " + str(n_samples) + "\n") + output_file.write("Mapping Tool: " + str(mapping_method) + "\n") if len(transform) > 0: transform_text = "Transform - " if transform == "qnorm": @@ -564,10 +569,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("Name,Chr,") if score_type.lower() == "-logP": score_type = "-logP" - if 'Mb' in markers[0]: - output_file.write("Mb," + score_type) - if 'cM' in markers[0]: - output_file.write("Cm," + score_type) + output_file.write(scale_string + "," + score_type) if "additive" in list(markers[0].keys()): output_file.write(",Additive") if "dominance" in list(markers[0].keys()): @@ -575,11 +577,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("\n") for i, marker in enumerate(markers): output_file.write(marker['name'] + "," + str(marker['chr']) + ",") - if 'Mb' in marker: - output_file.write(str(marker['Mb']) + ",") - if 'cM' in marker: - output_file.write(str(marker['cM']) + ",") - if "lod_score" in marker.keys(): + output_file.write(str(marker[scale_string]) + ",") + if score_type == "-logP": output_file.write(str(marker['lod_score'])) else: output_file.write(str(marker['lrs_value'])) |