adjust assignment scoring

src/isoform_assignment.py

@@ -228,10 +228,10 @@ def is_major_inconsistency(match_event_subtype):
     MatchEventSubtype.exon_elongation_left:0.1,
     MatchEventSubtype.exon_elongation_right:0.1,
     # intron retentions
-    MatchEventSubtype.intron_retention:0.5,
-    MatchEventSubtype.unspliced_intron_retention:0.5,
-    MatchEventSubtype.incomplete_intron_retention_left:0.75,
-    MatchEventSubtype.incomplete_intron_retention_right:0.75,
+    MatchEventSubtype.intron_retention:0.6,
+    MatchEventSubtype.unspliced_intron_retention:0.6,
+    MatchEventSubtype.incomplete_intron_retention_left:0.6,
+    MatchEventSubtype.incomplete_intron_retention_right:0.6,
     MatchEventSubtype.fake_micro_intron_retention:0.1,
     # major alternation
     # alternative donor/acceptor sites
@@ -246,37 +246,37 @@ def is_major_inconsistency(match_event_subtype):
     MatchEventSubtype.extra_intron_flanking_left:1,
     MatchEventSubtype.extra_intron_flanking_right:1,
     # significant exon elongation, more than allowed
-    MatchEventSubtype.major_exon_elongation_left:1,
-    MatchEventSubtype.major_exon_elongation_right:1,
+    MatchEventSubtype.major_exon_elongation_left:0.6,
+    MatchEventSubtype.major_exon_elongation_right:0.6,
     # other intron modifications
     MatchEventSubtype.intron_migration:1,
     MatchEventSubtype.intron_alternation_novel:1,
     MatchEventSubtype.intron_alternation_known:1,
     # mutually exclusive
-    MatchEventSubtype.mutually_exclusive_exons_novel:0.6,
-    MatchEventSubtype.mutually_exclusive_exons_known:0.6,
+    MatchEventSubtype.mutually_exclusive_exons_novel:0.8,
+    MatchEventSubtype.mutually_exclusive_exons_known:0.8,
     # exon skipping
     MatchEventSubtype.exon_skipping_known:1,
     MatchEventSubtype.exon_skipping_novel:1,
-    MatchEventSubtype.exon_merge_known:0.5,
-    MatchEventSubtype.exon_merge_novel:0.5,
+    MatchEventSubtype.exon_merge_known:0.75,
+    MatchEventSubtype.exon_merge_novel:0.75,
     # exon gain
     MatchEventSubtype.exon_gain_known:1,
     MatchEventSubtype.exon_gain_novel:1,
-    MatchEventSubtype.exon_detach_known:0.5,
-    MatchEventSubtype.exon_detach_novel:0.5,
+    MatchEventSubtype.exon_detach_known:0.75,
+    MatchEventSubtype.exon_detach_novel:0.75,
     MatchEventSubtype.terminal_exon_shift_known:0.5,
     MatchEventSubtype.terminal_exon_shift_novel:0.5,
     # other
     MatchEventSubtype.alternative_structure_novel:1,
     MatchEventSubtype.alternative_structure_known:1,
     # TTS and TSS
-    MatchEventSubtype.alternative_polya_site_left:0.75,
-    MatchEventSubtype.alternative_polya_site_right:0.75,
+    MatchEventSubtype.alternative_polya_site_left:0.6,
+    MatchEventSubtype.alternative_polya_site_right:0.6,
     MatchEventSubtype.internal_polya_left:0.5,
     MatchEventSubtype.internal_polya_right:0.5,
-    MatchEventSubtype.alternative_tss_left :0.75,
-    MatchEventSubtype.alternative_tss_right :0.75,
+    MatchEventSubtype.alternative_tss_left :0.6,
+    MatchEventSubtype.alternative_tss_right :0.6,
     MatchEventSubtype.correct_polya_site_left:0,
     MatchEventSubtype.correct_polya_site_right:0,
     MatchEventSubtype.aligned_polya_tail:0,