do not print . transcripts

ablab · Sep 13, 2023 · 71b652f · 71b652f
1 parent b1fc217
commit 71b652f
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/isoquant.py b/isoquant.py
@@ -140,6 +140,9 @@ def add_hidden_option(*args, **kwargs):  # show command only with --full-help
 
     parser.add_argument('--check_canonical', action='store_true', default=False,
                         help="report whether splice junctions are canonical")
+    add_additional_option("--keep_noncanonical", help="report transcripts for which the strand cannot be detected "
+                                                      "using canonical splice sites",
+                          action='store_true', default=False)
     parser.add_argument("--sqanti_output", help="produce SQANTI-like TSV output",
                         action='store_true', default=False)
     parser.add_argument("--count_exons", help="perform exon and intron counting", action='store_true', default=False)

diff --git a/src/graph_based_model_construction.py b/src/graph_based_model_construction.py
@@ -374,9 +374,14 @@ def construct_fl_isoforms(self):
                 #logger.debug("uuu Novel isoform %s has coverage: %d cutoff = %d, component cov = %d, max_coverage = %d"
                 #             % (new_transcript_id, count, novel_isoform_cutoff, component_coverage, self.intron_graph.max_coverage))
                 if count < novel_isoform_cutoff:
-                    pass #logger.debug("uuu Novel isoform %s has low coverage: %d\t%d" % (new_transcript_id, 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 (not polya_site or transcript_ss_strand == '.'):
-                    pass #logger.debug("uuu Avoiding single intron %s isoform: %d\t%s" % (new_transcript_id, count, str(path)))
+                    # 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.keep_noncanonical:
+                    logger.info("Avoiding unreliable transcript with %d exons" % len(novel_exons))
+                    pass
                 else:
                     if self.params.use_technical_replicas and \
                             len(set([a.read_group for a in self.path_storage.paths_to_reads[path]])) <= 1: