From d1d0a345d82ef72677fb7ceaf3b1160e229024d2 Mon Sep 17 00:00:00 2001
From: Brandon Seah <brandon_seah@tll.org.sg>
Date: Wed, 28 May 2025 17:48:48 +0800
Subject: [PATCH] DigitalSequenceBlock instead of list for hmmer

See https://github.com/MatthiasLienhard/isotools/issues/12
and https://github.com/althonos/pyhmmer/issues/87

pyhmmer>=0.11.1 will raise TypeError with unsupported types

If list can fit in memory, DigitalSequenceBlock should too
---
 src/isotools/domains.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/isotools/domains.py b/src/isotools/domains.py
index b2aff4e..4682b31 100644
--- a/src/isotools/domains.py
+++ b/src/isotools/domains.py
@@ -215,7 +215,11 @@ def get_hmmer_sequences(
                 )
                 sequences.append(text_seq.digitize(aa_alphabet))
                 seq_ids.append(seqnames)
-    return sequences, seq_ids
+    sequences_block = pyhmmer.easel.DigitalSequenceBlock(
+        alphabet=sequences[0].alphabet,
+        iterable=sequences,
+    )
+    return sequences_block, seq_ids
 
 
 #  function of isoseq.Transcriptome