Cleaning things up

Clinical-Genomics · Oct 18, 2024 · bc19f45 · bc19f45
1 parent 10d93f5
commit bc19f45
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Showing 2 changed files with 0 additions and 31 deletions.
diff --git a/genmod/commands/score_compounds.py b/genmod/commands/score_compounds.py
@@ -54,8 +54,6 @@ def compound(context, variant_file, silent, outfile, vep, threshold: int, penalt
     """
     logger.info('Running GENMOD score_compounds, version: {0}'.format(__version__))
 
-    print("Inside compounds")
-
     variant_file = get_file_handle(variant_file)
 
     start_time_analysis = datetime.now()
@@ -75,7 +73,6 @@ def compound(context, variant_file, silent, outfile, vep, threshold: int, penalt
 
     logger.info("Headers parsed")
 
-
     if not line.startswith('#'):
         variant_file = itertools.chain([line], variant_file)
     else:
@@ -159,8 +156,6 @@ def compound(context, variant_file, silent, outfile, vep, threshold: int, penalt
                                     results_queue=results
                                 )
 
-
-
         logger.debug("Put stop signs in the variant queue")
         for i in range(num_scorers):
             variant_queue.put(None)

diff --git a/genmod/score_variants/compound_scorer.py b/genmod/score_variants/compound_scorer.py
@@ -150,12 +150,6 @@ def _get_rankscore_normalization_bounds(variant_batch: Dict[str, Dict]) -> Dict[
         return variant_rankscore_normalization_bounds
 
     def run(self):
-
-
-        # THRESHOLD = 9
-        # PENALTY = 20
-
-
         """Run the consuming"""
         logger.info('%s: Starting!' % self.proc_name)
         # Check if there are any batches in the queue
@@ -191,11 +185,6 @@ def run(self):
                         #TODO check if correct family id
                         # Right now we assume that there is only one family in the vcf
 
-                        # print("INSIDE ")
-                        # print(family_rank_score)
-                        if family_rank_score[0] == '':
-                            continue
-
                         family_id = family_rank_score[0]
                         rank_score = float(family_rank_score[-1])
 
@@ -254,27 +243,17 @@ def run(self):
 
                             compound_rank_score = rank_scores[rank_score_type][compound_id]
 
-                            if variant['POS'] == "46602462":
-                                print(f"Compound: {compound_id} score: {compound_rank_score}")
-
-
 
                             if compound_rank_score > get_rank_score(rank_score_type=rank_score_type,
                                                                     threshold=self.threshold,
                                                                     min_rank_score_value=variant_rankscore_normalization_bounds[variant_id][0],
                                                                     max_rank_score_value=variant_rankscore_normalization_bounds[variant_id][1]
                                                                     ):
                                 only_low = False
-                                if variant['POS'] == "46602462":
-                                    print(f"Hit something")
                         logger.debug("Setting only_low to {0}".format(only_low))
 
                         if (correct_score and only_low):
 
-                            if variant['POS'] == "46602462":
-                                print(f"Aha, didn't hit anything, penalizing")
-
-
                             logger.debug("correcting rank score for {0}".format(
                                 variant_id))
                             current_rank_score -= get_rank_score_as_magnitude(rank_score_type=rank_score_type,
@@ -309,8 +288,6 @@ def run(self):
                         variant['info_dict'][f'{rank_score_type}'] = new_rank_score_string
                         variant['info_dict'][f'Compounds{rank_score_type.strip("RankScore")}'] = new_compound_string
 
-                        if variant['POS'] == "46602462":
-                            print("Point 1")
                             # print(variant["info_dict"])
                             # raise ValueError(variant)
                         # import sys
@@ -336,9 +313,6 @@ def run(self):
                             variant_dict=variant
                         )
 
-                    if variant['POS'] == "46602462":
-                        print("Point 2")
-                        # print(variant["info_dict"])
                 logger.debug("Putting variant in results_queue")
 
                 self.results_queue.put(variant)