Fix mut sequence output

Author: ThijsMaas

Diff for: 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 for: 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 for: 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"