Refactoring complete

ncsa · Sep 19, 2024 · 62821b9 · 62821b9
1 parent 19b74f0
commit 62821b9
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Showing 4 changed files with 6 additions and 613 deletions.
diff --git a/neat/models/__init__.py b/neat/models/__init__.py
@@ -1 +1,3 @@
-from .models import *
+from .error_models import *
+from .mutation_model import *
+from .fragment_model import *
diff --git a/neat/models/error_models.py b/neat/models/error_models.py
@@ -20,7 +20,8 @@
 from .variant_models import InsertionModel, DeletionModel, SnvModel
 
 __all__ = [
-    "ErrorContainer"
+    "ErrorContainer",
+    "SequencingErrorModel"
 ]
 
 _LOG = logging.getLogger(__name__)

diff --git a/neat/models/fragment_model.py b/neat/models/fragment_model.py
@@ -4,35 +4,19 @@
 must have a corresponding model in order to be fully implemented.
 """
 
-import re
 import logging
-import abc
-import sys
 
 from numpy.random import Generator
-from Bio.Seq import Seq
-from Bio import SeqRecord
 
-from neat import variants
-
-from ..common import TRINUC_IND, ALLOWED_NUCL, NUC_IND, DINUC_IND
-from .default_mutation_model import *
 from .default_sequencing_error_model import *
 
 __all__ = [
-    "MutationModel",
-    "SequencingErrorModel",
-    "FragmentLengthModel",
-    "InsertionModel",
-    "DeletionModel",
-    "SnvModel",
-    "ErrorContainer"
+    "FragmentLengthModel"
 ]
 
 _LOG = logging.getLogger(__name__)
 
 
-
 class FragmentLengthModel:
     """
     A model of the fragment length based on mean and standard deviation of the dataset. Used both