use copy.copy instead of list.copy

openvax · Jul 3, 2016 · 549d4fd · 549d4fd
1 parent 7a81cb3
commit 549d4fd
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/isovar/assembly.py b/isovar/assembly.py
@@ -16,6 +16,8 @@
 
 from collections import defaultdict
 import logging
+# I'd rather just use list.copy but Python 2.7 doesn't support it
+from copy import copy
 
 from .read_helpers import group_unique_sequences
 from .variant_sequences import VariantSequence
@@ -172,7 +174,7 @@ def iterative_assembly(
     shorter sequences onto every longer sequence which contains them.
     """
     for i in range(n_merge_iters):
-        previous_sequences = variant_sequences.copy()
+        previous_sequences = copy(variant_sequences)
         variant_sequences = greedy_merge(
             variant_sequences,
             min_overlap_size=min_overlap_size)

diff --git a/isovar/dataframe_builder.py b/isovar/dataframe_builder.py
@@ -33,7 +33,8 @@ def __init__(
             exclude=set([]),
             converters={},
             rename_dict={},
-            variant_columns=True):
+            variant_columns=True,
+            convert_collections_to_size=True):
         """
         Parameters
         ----------
@@ -56,11 +57,17 @@ def __init__(
 
         variant_columns : bool
             If True, then add four columns for fields of a Variant: chr/pos/ref/alt
+
+        convert_collections_to_size : bool
+            If a value is a built-in collection (list, tuple, or set) then
+            transform it to the size of that collection. If this option is False
+            then collection values cause a runtime error.
         """
         self.element_class = element_class
         self.rename_dict = rename_dict
         self.converters = converters
         self.variant_columns = variant_columns
+        self.convert_collections_to_size = convert_collections_to_size
 
         # remove specified field names without changing the order of the others
         self.original_field_names = [
@@ -114,7 +121,7 @@ def add(self, variant, element):
                 fn = self.converters[name]
                 value = fn(value)
 
-            if isinstance(value, (tuple, list, set)):
+            if isinstance(value, (tuple, list, set)) and self.convert_collections_to_size:
                 value = len(value)
             elif not isinstance(value, VALID_ELEMENT_TYPES):
                 raise ValueError(