diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 67 |
1 files changed, 4 insertions, 63 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index d18f6a7b..495678e9 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -46,70 +46,11 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n if cofactors: post_data["addcovar"] = True - out_file = requests.post(GN3_RQTL_URL, data=post_data).json()['output_file'] - + rqtl_output = requests.post(GN3_RQTL_URL, data=post_data).json() if num_perm > 0: - perm_results, suggestive, significant = process_perm_results(out_file) - return perm_results, suggestive, significant, process_rqtl_results(out_file) + return rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'], rqtl_output['results'] else: - return process_rqtl_results(out_file) - - -def process_rqtl_results(out_file: str) -> List: - """Given the output filename, read in results and - return as a list of dictionaries representing each - marker - - """ - - marker_obs = [] - # Later I should probably redo this using csv.read to avoid the - # awkwardness with removing quotes with [1:-1] - with open(GN3_TMP_PATH + "/output/" + out_file, "r") as the_file: - for line in the_file: - line_items = line.split(",") - if line_items[1][1:-1] == "chr" or not line_items: - # Skip header line - continue - else: - # Convert chr to int if possible - try: - the_chr = int(line_items[1][1:-1]) - except: - the_chr = line_items[1][1:-1] - this_marker = { - "name": line_items[0][1:-1], - "chr": the_chr, - "cM": float(line_items[2]), - "Mb": float(line_items[2]), - "lod_score": float(line_items[3]) - } - marker_obs.append(this_marker) - - return marker_obs - - -def process_perm_results(out_file: str): - """Given base filename, read in R/qtl permutation output and calculate - suggestive and significant thresholds - - """ - perm_results = [] - with open(GN3_TMP_PATH + "/output/PERM_" + out_file, "r") as the_file: - for i, line in enumerate(the_file): - if i == 0: - # Skip header line - continue - else: - line_items = line.split(",") - perm_results.append(float(line_items[1])) - - logger.debug("PERM RESULTS:", perm_results) - - suggestive = np.percentile(np.array(perm_results), 67) - significant = np.percentile(np.array(perm_results), 95) - - return perm_results, suggestive, significant + return rqtl_output['results'] def get_hash_of_textio(the_file: TextIO) -> str: @@ -182,4 +123,4 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict: cofactors[cofactor_name].append(sample_value) else: cofactors[cofactor_name].append("NA") - return cofactors
\ No newline at end of file + return cofactors |