diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/rqtl.py | 3 | ||||
| -rw-r--r-- | gn3/computations/rqtl.py | 86 |
2 files changed, 64 insertions, 25 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index 6548e1a..85b2460 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -6,7 +6,8 @@ from flask import current_app from flask import jsonify from flask import request -from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, process_rqtl_pairscan, process_perm_output +from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, \ + process_rqtl_pairscan, process_perm_output from gn3.computations.gemma import do_paths_exist rqtl = Blueprint("rqtl", __name__) diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index bb28dc3..e81aba3 100644 --- a/gn3/computations/rqtl.py +++ b/gn3/computations/rqtl.py @@ -118,16 +118,19 @@ def pairscan_for_figure(file_name: str) -> Dict: return figure_data -def pairscan_for_table(file_name: str, geno_file: str) -> List: - """Given an output file name, read in R/qtl pair-scan results and return - a list of results to be used when generating the results table (which will include marker names)""" - table_data = [] - # Open the map file with the list of markers/pseudomarkers and create list of marker obs +def get_marker_list(map_file: str) -> List: + """ + Open the map file with the list of markers/pseudomarkers and create list of marker obs + + PARAMETERS: + map_file: The map file output by R/qtl containing marker/pseudomarker positions + """ + + marker_list = [] with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), - "output", "MAP_" + file_name), "r") as the_file: - marker_list = [] - for i, line in enumerate(the_file.readlines()[1:]): + "output", map_file), "r") as map_fh: + for line in map_fh.readlines()[1:]: line_items = [item.rstrip('\n') for item in line.split(",")] this_marker = { 'name': line_items[0], @@ -137,37 +140,72 @@ def pairscan_for_table(file_name: str, geno_file: str) -> List: marker_list.append(this_marker) - # Get the list of original markers from the .geno file - original_markers = build_marker_pos_dict(geno_file) + return marker_list - # Open the file with the actual results and write the results as - # they will be displayed in the results table +def generate_table_rows(results_file: str, marker_list: List, original_markers: Dict) -> List: + """ + Open the file with the actual R/qtl pair-scan results and write them as + they will be displayed in the results table + + PARAMETERS: + results_file: The filename containing R/qtl pair-scan results + marker_list: List of marker/pseudomarker names/positions from results + original_markers: Dict of markers from the .geno file, for finding proximal/distal + markers to each pseudomarker + """ + + table_data = [] with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), - "output", file_name), "r") as the_file: + "output", results_file), "r") as the_file: for i, line in enumerate(the_file.readlines()[1:]): marker_1 = marker_list[i] - proximal1, distal1 = find_nearest_marker(marker_1['chr'], marker_1['pos'], original_markers) + marker_1['proximal'], marker_1['distal'] = find_nearest_marker(marker_1['chr'], + marker_1['pos'], + original_markers) line_items = [item.rstrip('\n') for item in line.split(",")] for j, item in enumerate(line_items[1:]): marker_2 = marker_list[j] - proximal2, distal2 = find_nearest_marker(marker_2['chr'], marker_2['pos'], original_markers) + marker_2['proximal'], marker_2['distal'] = find_nearest_marker(marker_2['chr'], + marker_2['pos'], + original_markers) try: lod_score = f"{float(item):.3f}" - except: + except ValueError: lod_score = f"{item}" - this_line = { - 'proximal1': proximal1, - 'distal1': distal1, + + table_data.append({ + 'proximal1': marker_1['proximal'], + 'distal1': marker_1['distal'], 'pos1': f"Chr {marker_1['chr']} @ {float(marker_1['pos']):.1f} cM", 'lod': lod_score, - 'proximal2': proximal2, - 'distal2': distal2, + 'proximal2': marker_2['proximal'], + 'distal2': marker_2['distal'], 'pos2': f"Chr {marker_2['chr']} @ {float(marker_2['pos']):.1f} cM" - } + }) + + return table_data + +def pairscan_for_table(file_name: str, geno_file: str) -> List: + """ + Read in R/qtl pair-scan results and return as List representing + table row contents + + PARAMETERS: + file_name: The filename containing R/qtl pair-scan results + geno_file: Filename of the genotype file (used to get marker positions) + """ - table_data.append(this_line) + # Open the map file with the list of markers/pseudomarkers and create list of marker obs + marker_list = get_marker_list("MAP_" + file_name) + + # Get the list of original markers from the .geno file + original_markers = build_marker_pos_dict(geno_file) + + # Open the file with the actual results and write the results as + # they will be displayed in the results table + table_data = generate_table_rows(file_name, marker_list, original_markers) - return sorted(table_data, key = lambda i: float(i['lod']), reverse=True)[:500] + return sorted(table_data, key=lambda i: float(i['lod']), reverse=True)[:500] def build_marker_pos_dict(genotype_file: str) -> Dict: """Gets list of markers and their positions from .geno file |