diff --git a/src/graph_based_model_construction.py b/src/graph_based_model_construction.py index 08fed3f9..a4b15862 100644 --- a/src/graph_based_model_construction.py +++ b/src/graph_based_model_construction.py @@ -270,7 +270,7 @@ def filter_transcripts(self): continue if len(model.exon_blocks) <= 2: - mapq = self.mapping_quality(model) + mapq = self.mapping_quality(model.transcript_id) #logger.debug("Novel model %s has quality %.2f" % (model.transcript_id, mapq)) if mapq < self.params.simple_models_mapq_cutoff: #logger.debug("Novel model %s has poor quality" % model.transcript_id) @@ -286,11 +286,11 @@ def filter_transcripts(self): self.transcript_model_storage = filtered_storage self.transcript_counter.add_confirmed_features(confirmed_transcipt_ids) - def mapping_quality(self, model): + def mapping_quality(self, transcript_id): mapq = 0 - for a in self.transcript_read_ids[model.transcript_id]: + for a in self.transcript_read_ids[transcript_id]: mapq += a.mapping_quality - return mapq / len(self.transcript_read_ids[model.transcript_id]) + return mapq / len(self.transcript_read_ids[transcript_id]) def detect_similar_isoforms(self, model_storage): to_substitute = {}