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-rw-r--r--gn3/api/rqtl.py3
-rw-r--r--gn3/computations/rqtl.py86
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