types: Rename SplicingType to TranscriptVariant

Author: lisavader

src/geneml/outputs.py

@@ -52,7 +52,8 @@ def get_end_coordinate(end_value, offset=offset):
             f"{transcript.score:.3f}",
             strand,
             ".",
-            f"ID={transcript_id};Parent={gene_id};SplicingType={transcript.splicing_type.name}",
+            (f"ID={transcript_id};Parent={gene_id};"
+             f"TranscriptVariant={transcript.transcript_variant.name}"),
         ))
 
         # exon records

src/geneml/splicing.py

@@ -1,6 +1,6 @@
 import logging
 
-from geneml.types import Exon, SplicingType, Transcript
+from geneml.types import Exon, Transcript, TranscriptVariant
 
 logger = logging.getLogger("geneml")
 
@@ -53,8 +53,8 @@ def get_introns_in_range(introns: list[tuple[int,int]], range: tuple[int,int], s
         raise ValueError(f"Invalid strand: {strand}")
 
 
-def get_alternative_splicing_type(primary: Transcript, alt: Transcript) -> SplicingType:
-    """Classify alternative splicing events between a primary and alternative transcript.
+def get_alternative_transcript_variant(primary: Transcript, alt: Transcript) -> TranscriptVariant:
+    """Classify the transcript variant of an alternative transcript.
 
     Compares intron junctions and terminal exon boundaries to detect exon skipping,
     alternative 3' and 5' splice sites, intron retention, and alternative first/last
@@ -66,7 +66,7 @@ def get_alternative_splicing_type(primary: Transcript, alt: Transcript) -> Splic
         alt: The alternative transcript being classified.
 
     Returns:
-        The assigned SplicingType for the alternative transcript.
+        The assigned TranscriptVariant for the alternative transcript.
     """
     assert primary.exons != alt.exons, (
         f"Identical transcripts: {primary.transcript_id} and {alt.transcript_id}"
@@ -110,9 +110,9 @@ def get_alternative_splicing_type(primary: Transcript, alt: Transcript) -> Splic
         raise ValueError(f"Invalid strand: {strand}")
 
     if alt_first != primary_first:
-        events.add(SplicingType.ALT_FIRST_EXON)
+        events.add(TranscriptVariant.ALT_FIRST_EXON)
     if alt_last != primary_last:
-        events.add(SplicingType.ALT_LAST_EXON)
+        events.add(TranscriptVariant.ALT_LAST_EXON)
 
     # 2. EXON SKIPPING
     for s, e in P:
@@ -121,7 +121,7 @@ def get_alternative_splicing_type(primary: Transcript, alt: Transcript) -> Splic
             s2, e2 = A[i + 1]
 
             if s1 == s and e2 == e:
-                events.add(SplicingType.EXON_SKIPPING)
+                events.add(TranscriptVariant.EXON_SKIPPING)
                 consumed_P.add((s, e))
                 consumed_A.add((s1, e1))
                 consumed_A.add((s2, e2))
@@ -132,7 +132,7 @@ def get_alternative_splicing_type(primary: Transcript, alt: Transcript) -> Splic
             s2, e2 = P[i + 1]
 
             if s1 == s and e2 == e:
-                events.add(SplicingType.EXON_SKIPPING)
+                events.add(TranscriptVariant.EXON_SKIPPING)
                 consumed_A.add((s, e))
                 consumed_P.add((s1, e1))
                 consumed_P.add((s2, e2))
@@ -148,18 +148,18 @@ def get_alternative_splicing_type(primary: Transcript, alt: Transcript) -> Splic
                 # Skip if this is in a terminal exon already recognized as alt event
                 at_alt_first_exon = (
                     ((s1, e1) == P[0] or (s2, e2) == A[0])
-                    and SplicingType.ALT_FIRST_EXON in events
+                    and TranscriptVariant.ALT_FIRST_EXON in events
                 )
                 at_alt_last_exon = (
                     ((s1, e1) == P[-1] or (s2, e2) == A[-1])
-                    and SplicingType.ALT_LAST_EXON in events
+                    and TranscriptVariant.ALT_LAST_EXON in events
                 )
                 if not (at_alt_first_exon or at_alt_last_exon):
-                    events.add(SplicingType.ALT_3_SPLICE_SITE)
+                    events.add(TranscriptVariant.ALT_3_SPLICE_SITE)
                 consumed_P.add((s1, e1))
                 consumed_A.add((s2, e2))
             if e1 == e2 and s1 != s2:
-                events.add(SplicingType.ALT_5_SPLICE_SITE)
+                events.add(TranscriptVariant.ALT_5_SPLICE_SITE)
                 consumed_P.add((s1, e1))
                 consumed_A.add((s2, e2))
 
@@ -168,13 +168,13 @@ def get_alternative_splicing_type(primary: Transcript, alt: Transcript) -> Splic
     remaining_A = (A_set - P_set) - consumed_A
 
     if remaining_P or remaining_A:
-        events.add(SplicingType.INTRON_RETENTION)
+        events.add(TranscriptVariant.INTRON_RETENTION)
 
     assert events, (
-        f"No splicing events detected between {primary.transcript_id} and {alt.transcript_id}; "
+        f"No events detected between {primary.transcript_id} and {alt.transcript_id}; "
         f"this should not happen"
     )
 
     if len(events) == 1:
         return events.pop()
-    return SplicingType.COMPLEX
+    return TranscriptVariant.COMPLEX

src/geneml/types.py

@@ -17,7 +17,7 @@
 GeneCallNumbaType = typeof(typed.List.empty_list(GeneEventNumbaType))
 
 
-class SplicingType(Enum):
+class TranscriptVariant(Enum):
     UNKNOWN = 0
     PRIMARY = 1
     INTRON_RETENTION = 2
@@ -52,7 +52,7 @@ class Transcript:
     exons: tuple[Exon, ...]
     group_id: int = -1
     transcript_id: str = ""
-    splicing_type: SplicingType = SplicingType.UNKNOWN
+    transcript_variant: TranscriptVariant = TranscriptVariant.UNKNOWN
 
     def __post_init__(self):
         if not self.exons:
@@ -66,17 +66,17 @@ def __post_init__(self):
     def set_transcript_id(self, transcript_id: str):
         self.transcript_id = transcript_id
 
-    def set_splicing_type(self, splicing_type: SplicingType):
-        self.splicing_type = splicing_type
+    def set_transcript_variant(self, transcript_variant: TranscriptVariant):
+        self.transcript_variant = transcript_variant
 
-    def classify_splicing_type(self, primary_transcript: 'Transcript'):
-        assert primary_transcript.splicing_type == SplicingType.PRIMARY
+    def classify_transcript_variant(self, primary_transcript: 'Transcript'):
+        assert primary_transcript.transcript_variant == TranscriptVariant.PRIMARY
 
         if self.exons == primary_transcript.exons:
-            return SplicingType.PRIMARY
+            return TranscriptVariant.PRIMARY
 
-        from geneml.splicing import get_alternative_splicing_type
-        return get_alternative_splicing_type(primary_transcript, self)
+        from geneml.splicing import get_alternative_transcript_variant
+        return get_alternative_transcript_variant(primary_transcript, self)
 
     def overlaps_with(self, other: 'Transcript', ignore_strand: bool = False) -> bool:
         # by default only consider overlaps on the same strand
@@ -107,8 +107,8 @@ def __post_init__(self):
 
             # First transcript always denotes the primary splicing type
             if i == 0:
-                transcript.set_splicing_type(SplicingType.PRIMARY)
+                transcript.set_transcript_variant(TranscriptVariant.PRIMARY)
                 primary = transcript
             else:
-                splicing_type = transcript.classify_splicing_type(primary)
-                transcript.set_splicing_type(splicing_type)
+                transcript_variant = transcript.classify_transcript_variant(primary)
+                transcript.set_transcript_variant(transcript_variant)