diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/rqtl.py | 87 |
1 files changed, 82 insertions, 5 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index 405b743..00e1db9 100644 --- a/gn3/computations/rqtl.py +++ b/gn3/computations/rqtl.py @@ -82,19 +82,96 @@ def process_rqtl_mapping(file_name: str) -> List: def process_rqtl_pairscan(file_name: str) -> List: """Given an output file name, read in R/qtl pair-scan results and return - a List of Lists representing the matrix of results + a list of both the JSON needed for the d3panels figure and a list of results + to be used when generating the results table (which will include marker names) """ - results = [] + + figure_data = pairscan_results_for_figure(file_name) + table_data = pairscan_results_for_table(file_name) + + return [figure_data, table_data] + +def pairscan_for_figure(file_name: str) -> Dict: + """Given an output file name, read in R/qtl pair-scan results and return + the JSON needed for the d3panels figure + + """ + figure_data = {} + + # Open the file with the actual results, written as a list of lists with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), "output", file_name), "r") as the_file: + lod_results = [] for i, line in enumerate(the_file): if i == 0: # Skip first line continue - line_items = line.split(",") - results.append(line_items[1:]) # Append all but first item in line + line_items = [item.rstrip('\n') for item in line.split(",")] + lod_results.append(line_items[1:]) # Append all but first item in line + figure_data['lod'] = lod_results + + # Open the map file with the list of markers/pseudomarkers and their positions + with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), + "output", "MAP_" + file_name), "r") as the_file: + chr_list = [] + pos_list = [] + for i, line in enumerate(the_file): + if i == 0: # Skip first line + continue + line_items = [item.rstrip('\n') for item in line.split(",")] + chr_list.append(line_items[1]) + pos_list.append(line_items[2]) + figure_data['chr'] = chr_list + figure_data['pos'] = pos_list + + return figure_data + + +def pairscan_for_table(file_name: 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 + 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:]): + line_items = [item.rstrip('\n') for item in line.split(",")] + this_marker = { + 'name': line_items[0], + 'chr': line_items[1][1:-1], # Strip quotes from beginning and end of chr string + 'pos': line_items[2] + } + + marker_list.append(this_marker) + + # Open the file with the actual results and write the results as + # they will be displayed in the results table + with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), + "output", file_name), "r") as the_file: + for i, line in enumerate(the_file.readlines()[1:]): + marker_1 = marker_list[i] + line_items = [item.rstrip('\n') for item in line.split(",")] + for j, item in enumerate(line_items[1:]): + marker_2 = marker_list[j] + try: + lod_score = f"{float(item):.3f}" + except: + lod_score = f"{item}" + this_line = { + 'marker1': f"{marker_1['name']}", + 'pos1': f"Chr {marker_1['chr']} @ {float(marker_1['pos']):.1f} cM", + 'lod': lod_score, + 'marker2': f"{marker_2['name']}", + 'pos2': f"Chr {marker_2['chr']} @ {float(marker_2['pos']):.1f} cM" + } + table_data.append(this_line) + + return table_data - return results def process_perm_output(file_name: str): """Given base filename, read in R/qtl permutation output and calculate |