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feat: add transcript.length #213

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feat: add transcript.length #213

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13 changes: 13 additions & 0 deletions genome_kit/genome_annotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -603,6 +603,19 @@ def utr3s(self): # pragma: no cover
mock_unreachable()
return [Utr()]

@property
def length(self) -> int:
"""The total length of this transcript, summing all exon lengths (includes UTRs)."""
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@s22chan s22chan Apr 21, 2026 •
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introns are part of a transcript... are we conflating this with transcriptome mrna?

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@ovesh ovesh Apr 21, 2026

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@gkaur can you comment on this?

The original request:

Currently, transcript length is calculated by iterating over the exons, computing the difference between each exon’s start and end positions, and summing those values. It would be much easier if this was recalculated and stored for each transcript.

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@gkaur gkaur Apr 21, 2026

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I was hoping to capture post processed transcript length based on exons and cdss components only

return sum(len(exon) for exon in self.exons)

@property
def length_cds(self) -> int:
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@s22chan s22chan Apr 21, 2026 •
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I feel like the naming will be confusing in code.

eg.
len(trans.cdss)
vs
trans.length_cds

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@ovesh ovesh Apr 21, 2026

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That's a reasonable concern. I'm coming up empty trying to think of a clearer alternative.

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@ovesh ovesh Apr 21, 2026

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How about .exonic_length and .coding_length?

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@gkaur gkaur Apr 21, 2026

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works for me!

"""The CDS-only length of this transcript, summing all CDS element lengths.

Returns 0 for non-coding transcripts.
"""
return sum(len(cds) for cds in self.cdss)

def __getstate__(self) -> bytes:
genome = self.annotation_genome
return pickle.dumps([genome, genome.transcripts.index_of(self)])
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6 changes: 2 additions & 4 deletions tests/test_genome_annotation.py
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@@ -1,11 +1,7 @@
# Copyright (C) 2016-2023 Deep Genomics Inc. All Rights Reserved.
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import gc
import os
import genome_kit
from genome_kit import Genome
from genome_kit import GenomeAnnotation
from genome_kit import GeneTable
Expand Down Expand Up @@ -476,6 +472,8 @@ def test_transcript_attributes(self):
self.assertEqual(len(tran.cdss), 4)
self.assertEqual(len(tran.utr5s), 1)
self.assertEqual(len(tran.utr3s), 1)
self.assertEqual(tran.length, 2895) # 515 + 227 + 197 + 1956
self.assertEqual(tran.length_cds, 2514) # 352 + 227 + 197 + 1738
self.assertIsInstance(tran, Interval)
self.assertIsInstance(tran.__repr__(), str)

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