diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 26 |
1 files changed, 24 insertions, 2 deletions
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 72844903..8f051c14 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -395,7 +395,7 @@ class RunMapping(object): 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_scale, self.score_type, self.transform, self.covariates, self.n_samples) with Bench("Trimming Markers for Figure"): if len(self.qtl_results) > 30000: @@ -504,14 +504,36 @@ class RunMapping(object): trimmed_genotype_data.append(new_genotypes) return trimmed_genotype_data -def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type): +def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples): with open(results_path, "w+") as output_file: output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n") output_file.write("Data Set: " + dataset.fullname + "\n") + output_file.write("N Samples: " + str(n_samples) + "\n") + if len(transform) > 0: + transform_text = "Transform - " + if transform == "qnorm": + transform_text += "Quantile Normalized" + elif transform == "log2" or transform == "log10": + transform_text += transform.capitalize() + elif transform == "sqrt": + transform_text += "Square Root" + elif transform == "zscore": + transform_text += "Z-Score" + elif transform == "invert": + transform_text += "Invert +/-" + else: + transform_text = "" + output_file.write(transform_text + "\n") if dataset.type == "ProbeSet": output_file.write("Gene Symbol: " + trait.symbol + "\n") output_file.write("Location: " + str(trait.chr) + " @ " + str(trait.mb) + " Mb\n") + if len(covariates) > 0: + output_file.write("Cofactors (dataset - trait):\n") + for covariate in covariates.split(","): + trait_name = covariate.split(":")[0] + dataset_name = covariate.split(":")[1] + output_file.write(dataset_name + " - " + trait_name + "\n") output_file.write("\n") output_file.write("Name,Chr,") if score_type.lower() == "-logP": |