Fixes pylint errors

2 files changed, 62 insertions, 25 deletions

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index b6c04eb..70ebe12 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 4327cac..65ee6de 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -118,17 +118,18 @@ def pairscan_for_figure(file_name: str) -> Dict:
 
     return figure_data
 
+def get_marker_list(map_file: str) -> List:
+    """
+    Open the map file with the list of markers/pseudomarkers and create list of marker obs
 
-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 = []
+    PARAMETERS:
+    map_file: The map file output by R/qtl containing marker/pseudomarker positions
+    """
 
-    # Open the map file with the list of markers/pseudomarkers and create list of marker obs
+    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],
@@ -138,37 +139,72 @@ 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"
-                }
+                })
 
-                table_data.append(this_line)
+    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)
+    """
+
+    # 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