fix SS strand filtering

ablab · Apr 9, 2024 · 6117cff · 6117cff
1 parent 891f346
commit 6117cff
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/src/dataset_processor.py b/src/dataset_processor.py
@@ -540,7 +540,7 @@ def process_assigned_reads(self, sample, dump_filename):
             reverse=True
         )
         logger.info("Processing assigned reads " + sample.prefix)
-        logger.info("  Transcript models construction is turned %s" %
+        logger.info("Transcript models construction is turned %s" %
                     ("off" if self.args.no_model_construction else "on"))
 
         # set up aggregators and outputs

diff --git a/src/graph_based_model_construction.py b/src/graph_based_model_construction.py
@@ -377,7 +377,8 @@ def construct_fl_isoforms(self):
                 if count < novel_isoform_cutoff:
                     # logger.debug("uuu Novel isoform %s has low coverage: %d\t%d" % (new_transcript_id, count, novel_isoform_cutoff))
                     pass
-                elif len(novel_exons) == 2 and self.params.require_monointronic_polya and not polya_site:
+                elif (len(novel_exons) == 2 and
+                      ((self.params.require_monointronic_polya and not polya_site) or transcript_ss_strand == '.')):
                     # logger.debug("uuu Avoiding single intron %s isoform: %d\t%s" % (new_transcript_id, count, str(path)))
                     pass
                 elif transcript_strand == '.' and not self.params.report_unstranded: