From 823fd759d2a211000ba6e2a49141b6dbdaa8f640 Mon Sep 17 00:00:00 2001
From: Thijs <tpwmaas@gmail.com>
Date: Mon, 5 Feb 2024 19:45:19 +0100
Subject: [PATCH] Fix mut sequence output

---
 iss/error_models/__init__.py | 2 +-
 iss/generator.py             | 6 +++---
 iss/test/test_error_model.py | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/iss/error_models/__init__.py b/iss/error_models/__init__.py
index 17ea70f..413303a 100644
--- a/iss/error_models/__init__.py
+++ b/iss/error_models/__init__.py
@@ -78,7 +78,7 @@ def mut_sequence(self, record, orientation):
                 'reverse'
 
         Returns:
-            Seq: a sequence
+            SeqRecord: the read record with substitution errors
         """
 
         # get the right subst_matrix
diff --git a/iss/generator.py b/iss/generator.py
index 2387e54..1b47ca7 100644
--- a/iss/generator.py
+++ b/iss/generator.py
@@ -155,7 +155,7 @@ def simulate_read(record, error_model, i, cpu_number, sequence_type):
     # add the indels, the qual scores and modify the record accordingly
     forward.seq = error_model.introduce_indels(forward, "forward", sequence, bounds)
     forward = error_model.introduce_error_scores(forward, "forward")
-    forward.seq = error_model.mut_sequence(forward, "forward")
+    forward = error_model.mut_sequence(forward, "forward")
 
     # generate the reverse read
     # assign start position reverse read
@@ -187,7 +187,7 @@ def simulate_read(record, error_model, i, cpu_number, sequence_type):
     # add the indels, the qual scores and modify the record accordingly
     reverse.seq = error_model.introduce_indels(reverse, "reverse", sequence, bounds)
     reverse = error_model.introduce_error_scores(reverse, "reverse")
-    reverse.seq = error_model.mut_sequence(reverse, "reverse")
+    reverse = error_model.mut_sequence(reverse, "reverse")
 
     return (forward, reverse, forward.annotations["mutations"] + reverse.annotations["mutations"])
 
@@ -235,7 +235,7 @@ def worker_iterator(work, error_model, cpu_number, worker_prefix, seed, sequence
         random.seed(seed + cpu_number)
         np.random.seed(seed + cpu_number)
 
-    with forward_handle, reverse_handle:
+    with forward_handle, reverse_handle, mutation_handle:
         for record, n_pairs, mode in work:
             simulate_reads(
                 record=record,
diff --git a/iss/test/test_error_model.py b/iss/test/test_error_model.py
index 6835665..fa7d863 100644
--- a/iss/test/test_error_model.py
+++ b/iss/test/test_error_model.py
@@ -52,7 +52,7 @@ def test_mut_sequence():
 
     read = SeqRecord(Seq(str("AAAAA" * 25)), id="read_1", description="test read")
     read.letter_annotations["phred_quality"] = [5] * 125
-    read.seq = err_mod.mut_sequence(read, "forward")
+    read = err_mod.mut_sequence(read, "forward")
     assert str(read.seq[:10]) == "AAAACAGAAA"