Merge pull request #4 from Edinburgh-Genome-Foundry/dev

Biopython v1.78 compatibility

LICENCE.txt

@@ -1,8 +1,4 @@
-
-The MIT License (MIT)
-[OSI Approved License]
-
-The MIT License (MIT)
+MIT License
 
 Copyright (c) 2020 Edinburgh Genome Foundry
 
@@ -13,13 +9,13 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

dnacauldron/Fragment/Fragment.py

@@ -19,7 +19,7 @@ def from_biopython_record(biopython_record):
 
     def plot(self, ax=None):
         """Plot the fragment and its features on a Matplotlib ax.
-        
+
         This creates a new ax if no ax is provided. The ax is returned at the
         end.
         """
@@ -37,9 +37,9 @@ def reverse_complement(self):
 
     def to_standard_string(self):
         """Return a standard string to represent and identify the fragment.
-        
+
         This method is used to standardize and recognize similar FragmentChain
-        instances. 
+        instances.
         """
 
         return str(self.seq)
@@ -53,13 +53,11 @@ def create_homology_annotation(
             "ApEinfo_fwdcolor": color,
         }
         return SeqFeature(
-            FeatureLocation(start, end),
-            type=annotation_type,
-            qualifiers=qualifiers,
+            FeatureLocation(start, end), type=annotation_type, qualifiers=qualifiers,
         )
-    
+
     def text_representation_in_plots(self):
         return r"$\bf{%s}$" % self.original_part.id
-    
-    def as_bioptyhon_record(self):
+
+    def as_biopython_record(self):
         return self

dnacauldron/Fragment/HomologousFragment/HomologousFragment.py

@@ -1,27 +1,33 @@
 from copy import deepcopy
 from Bio.SeqRecord import SeqRecord
 from ..Fragment import Fragment
-from Bio.Alphabet import DNAAlphabet
+
+try:
+    # Biopython <1.78
+    from Bio.Alphabet import DNAAlphabet
+
+    has_dna_alphabet = True
+except ImportError:
+    # Biopython >=1.78
+    has_dna_alphabet = False
+
 from ...biotools import set_record_topology, crop_record_with_saddling_features
 
 
 class HomologousFragment(Fragment):
     @staticmethod
     def from_biopython_record(biopython_record):
-        """Convert a biopython record into a HomologousFragment (class change).
+        """Convert a Biopython record into a HomologousFragment (class change).
         """
         new_record = deepcopy(biopython_record)
         new_record.original_part = biopython_record
         new_record.__class__ = HomologousFragment
         return new_record
 
     def circularized(
-        self,
-        homology_checker,
-        annotate_homology=False,
-        annotation_type="homology",
+        self, homology_checker, annotate_homology=False, annotation_type="homology",
     ):
-        """Return the biopython record obtained by cirularizing the result.
+        """Return the Biopython record obtained by cirularizing the result.
 
         Only works if the left and right sticky ends are compatible. The
         return is a simple Biopython record where the sticky end has been
@@ -33,8 +39,10 @@ def circularized(
             annotate_homology=True,
             annotation_type="homology",
         )
+
         def only_parts_indicators(feature):
             return feature.qualifiers.get("indicates_part", False)
+
         result = crop_record_with_saddling_features(
             record=double_self,
             start=len(self),
@@ -64,13 +72,11 @@ def _push_source_features(self, homology_size, side="left"):
     def will_clip_in_this_order_with(self, other_fragment, homology_checker):
         """Return whether the fragment will assemble with anoter via homology
         recombination.
-        
+
         homology_checker should be an HomologyChecker instance definining the
         homology conditions.
         """
-        homology_size = homology_checker.find_end_homologies(
-            self, other_fragment
-        )
+        homology_size = homology_checker.find_end_homologies(self, other_fragment)
         return homology_size > 0
 
     def assemble_with(
@@ -82,16 +88,16 @@ def assemble_with(
     ):
         """Return the fragment resulting from the assembly of this fragment
         with another, in that order.
-        
+
         Parameters
         ----------
-        
+
         fragment
-          The other parameter to assemble with
-        
+          The other parameter to assemble with.
+
         homology_checker
           An HomologyChecker instance definining the homology conditions.
-        
+
         annotate_homology
           If true, homologies will have an annotation in the final, predicted
           construct records.
@@ -130,30 +136,25 @@ def only_parts_indicators(feature):
 
     @staticmethod
     def assemble(
-        fragments,
-        homology_checker,
-        circularize=False,
-        annotate_homologies=False,
+        fragments, homology_checker, circularize=False, annotate_homologies=False,
     ):
         """Return the record obtained by assembling the fragments.
 
         Parameters
         ----------
 
         fragments
-          List of HomologousFragments to assemble
+          List of HomologousFragments to assemble.
 
         homology_checker
           An HomologyChecker instance definining the homology conditions.
-          
+
         circularize
           True to also assemble the end flanks of the final construct.
 
         annotate_homologies
            If true, homologies will have an annotation in the final, predicted
            construct records.
-
-
         """
         result = fragments[0]
         for fragment in fragments[1:]:
@@ -167,5 +168,9 @@ def assemble(
                 annotate_homology=annotate_homologies,
                 homology_checker=homology_checker,
             )
-        result.seq.alphabet = DNAAlphabet()
+
+        if has_dna_alphabet:  # Biopython <1.78
+            result.seq.alphabet = DNAAlphabet()
+        result.annotations["molecule_type"] = "DNA"
+
         return result

dnacauldron/Fragment/StickyEndFragment/StickyEnd.py

@@ -1,6 +1,16 @@
 from Bio.Seq import Seq
+
+try:
+    # Biopython <1.78
+    from Bio.Alphabet import DNAAlphabet
+
+    has_dna_alphabet = True
+except ImportError:
+    # Biopython >=1.78
+    has_dna_alphabet = False
 from ...biotools import sequence_to_biopython_record, annotate_record
 
+
 class StickyEnd(Seq):
     """A class to represent the sticky end of a sequence.
 
@@ -10,10 +20,10 @@ class StickyEnd(Seq):
     ----------
 
     data
-      A DNA sequence in ATGC format
+      A DNA sequence in ATGC format.
 
     strand
-      The strand (+1 or -1) on which the protusion is
+      The strand (+1 or -1) on which the protusion is.
 
     **k
       Optional keyword arguments for the sequence, such as ``alphabet`` etc.
@@ -24,11 +34,15 @@ def __init__(self, data, strand, **k):
         self.strand = strand
 
     def reverse_complement(self):
-        return StickyEnd(
-            str(Seq.reverse_complement(self)),
-            strand=-self.strand,
-            alphabet=self.alphabet,
-        )
+
+        if has_dna_alphabet:  # Biopython <1.78
+            return StickyEnd(
+                str(Seq.reverse_complement(self)),
+                strand=-self.strand,
+                alphabet=self.alphabet,
+            )
+        else:
+            return StickyEnd(str(Seq.reverse_complement(self)), strand=-self.strand,)
 
     def __repr__(self):
         return "%s(%s)" % (Seq.__str__(self), {1: "+", -1: "-"}[self.strand])
@@ -40,10 +54,9 @@ def will_clip_directly_with(self, other):
             and (self.strand == -other.strand)
             and (str(self) == str(other))
         )
-    
+
     def as_biopython_record(self):
         record = sequence_to_biopython_record(str(self))
         sign = "+" if self.strand == 1 else "-"
         annotate_record(record, label="(%s) strand" % sign)
         return record
-