diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 25 |
1 files changed, 16 insertions, 9 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 495678e9..09afb8d1 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -23,7 +23,7 @@ GN3_TMP_PATH = "/export/local/home/zas1024/genenetwork3/tmp" def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, cofactors): """Run R/qtl by making a request to the GN3 endpoint and reading in the output file(s)""" - pheno_file = write_phenotype_file(trait_name, samples, vals, cofactors) + pheno_file = write_phenotype_file(trait_name, samples, vals, dataset, cofactors, perm_strata_list) if dataset.group.genofile: geno_file = locate(dataset.group.genofile, "genotype") else: @@ -46,6 +46,9 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n if cofactors: post_data["addcovar"] = True + if perm_strata_list: + post_data["pstrata"] = True + rqtl_output = requests.post(GN3_RQTL_URL, data=post_data).json() if num_perm > 0: return rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'], rqtl_output['results'] @@ -66,12 +69,12 @@ def write_phenotype_file(trait_name: str, samples: List[str], vals: List, dataset_ob, - cofactors: Optional[str] = None) -> TextIO: + cofactors: Optional[str] = None, + perm_strata_list: Optional[List] = None) -> TextIO: """Given trait name, sample list, value list, dataset ob, and optional string representing cofactors, return the file's full path/name """ - cofactor_data = cofactors_to_dict(cofactors, dataset_ob, samples) pheno_file = io.StringIO() @@ -79,6 +82,8 @@ def write_phenotype_file(trait_name: str, header_row = ["Samples", trait_name] header_row += [cofactor for cofactor in cofactor_data] + if perm_strata_list: + header_row.append("Strata") writer.writerow(header_row) for i, sample in enumerate(samples): @@ -89,6 +94,8 @@ def write_phenotype_file(trait_name: str, this_row.append("NA") for cofactor in cofactor_data: this_row.append(cofactor_data[cofactor][i]) + if perm_strata_list: + this_row.append(perm_strata_list[i]) writer.writerow(this_row) hash_of_file = get_hash_of_textio(pheno_file) @@ -106,21 +113,21 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict: and list of samples, return cofactor data as a Dict """ - cofactors = {} + cofactor_dict = {} if cofactors: dataset_ob.group.get_samplelist() sample_list = dataset_ob.group.samplelist for cofactor in cofactors.split(","): cofactor_name, cofactor_dataset = cofactor.split(":") - if cofactor_dataset == this_dataset.name: - cofactors[cofactor_name] = [] + if cofactor_dataset == dataset_ob.name: + cofactor_dict[cofactor_name] = [] trait_ob = create_trait(dataset=dataset_ob, name=cofactor_name) sample_data = trait_ob.data for index, sample in enumerate(samples): if sample in sample_data: sample_value = sample_data[sample].value - cofactors[cofactor_name].append(sample_value) + cofactor_dict[cofactor_name].append(sample_value) else: - cofactors[cofactor_name].append("NA") - return cofactors + cofactor_dict[cofactor_name].append("NA") + return cofactor_dict |