Merge pull request #96 from ginkgobioworks/include-feature-sequence

add sequence to feature and option to get in api

src/edge/models/chunk.py

@@ -1,6 +1,7 @@
 import gzip
 import json
 
+from Bio.Seq import Seq
 from django.db import models
 from django.db import transaction
 
@@ -58,7 +59,6 @@ def from_chunk_feature_and_location_array(chunk_feature_locs):
                            (t[0].feature.strand if t[0].feature.strand is not None else 1)
                            * t[0].feature_base_first)
         )
-
         annotations = []
         for cf, fcl in chunk_feature_locs:
             if (
@@ -300,6 +300,17 @@ class Meta:
     def set_qualifiers(self, qualifiers):
         self._qualifiers = json.dumps(qualifiers)
 
+    @property
+    def sequence(self):
+        seq = ''
+        cfs = self.chunk_feature_set.all()
+        for cf in sorted(cfs, key=lambda cf: cf.feature_base_first):
+            seq += cf.chunk.get_sequence()
+        # Reverse complement if on negative strand
+        return str(
+            Seq(seq).reverse_complement()
+        ) if self.strand is not None and self.strand < 0 else seq
+
     @property
     def qualifiers(self):
         if self._qualifiers is not None:

src/edge/tests/test_feature.py

@@ -0,0 +1,17 @@
+from django.test import TestCase
+
+from edge.models import Fragment
+
+
+class FeatureTests(TestCase):
+    def setUp(self):
+        self.root_sequence = "agttcgaggctga"
+        self.root = Fragment.create_with_sequence("Foo", self.root_sequence)
+
+    def test_sequence_positive_strand(self):
+        feature = self.root.annotate(3, 5, "A1", "gene", 1)
+        self.assertEqual(feature.sequence, "ttc")
+
+    def test_sequence_negative_strand(self):
+        feature = self.root.annotate(3, 5, "A1", "gene", -1)
+        self.assertEqual(feature.sequence, "gaa")

src/edge/views.py

@@ -193,8 +193,8 @@ def on_get(self, request, fragment_id):
 
 class FragmentAnnotationsView(ViewBase):
     @staticmethod
-    def to_dict(annotation):
-        return dict(
+    def to_dict(annotation, include_feature_sequence=False):
+        result = dict(
             base_first=annotation.base_first,
             base_last=annotation.base_last,
             strand=annotation.feature.strand,
@@ -212,16 +212,21 @@ def to_dict(annotation):
             qualifiers=annotation.feature.qualifiers,
             feature_full_length=annotation.feature.length
         )
+        if include_feature_sequence:
+            result['feature']['sequence'] = annotation.feature.sequence
+        return result
 
     def on_get(self, request, fragment_id):
         q_parser = RequestParser()
         q_parser.add_argument("f", field_type=int, location="get")
         q_parser.add_argument("l", field_type=int, location="get")
         q_parser.add_argument("m", field_type=int, location="get")
+        q_parser.add_argument("include_feature_sequence", field_type=str, default='false', location="get")
         args = q_parser.parse_args(request)
         f = args["f"]
         ll = args["l"]
         m = args["m"]
+        include_feature_sequence = args["include_feature_sequence"].lower() == "true"
 
         fragment = get_fragment_or_404(fragment_id)
         annotations = fragment.indexed_fragment().annotations(bp_lo=f, bp_hi=ll)
@@ -234,7 +239,9 @@ def on_get(self, request, fragment_id):
                 annotations = new_a
             annotations = to_return
         return [
-            FragmentAnnotationsView.to_dict(annotation) for annotation in annotations
+            FragmentAnnotationsView.to_dict(
+                annotation, include_feature_sequence=include_feature_sequence
+            ) for annotation in annotations
         ]
 
     @transaction.atomic()
@@ -580,9 +587,13 @@ def on_post(self, request, genome_id):
 
         parser = RequestParser()
         parser.add_argument("primers", field_type=list, required=True, location="json")
+        parser.add_argument(
+            "include_feature_sequence", field_type=bool, required=False, default=False, location="json"
+        )
 
         args = parser.parse_args(request)
         primers = args["primers"]
+        include_feature_sequence = args["include_feature_sequence"]
 
         if len(primers) != 2:
             raise Exception("Expecting two primers, got %s" % (primers,))
@@ -593,7 +604,7 @@ def on_post(self, request, genome_id):
         # Convert annotations in template_info to dictionary.
         if template_info and "annotations" in template_info:
             template_info["annotations"] = [
-                FragmentAnnotationsView.to_dict(annotation)
+                FragmentAnnotationsView.to_dict(annotation, include_feature_sequence=include_feature_sequence)
                 for annotation in template_info["annotations"]
             ]
         r = (