Merge pull request #29 from ginkgobioworks/fix-export

Fix export for negative strand

setup.py

@@ -124,8 +124,11 @@ def run(self):
     include_package_data=True,
     zip_safe=True,
 
+    # Django has to be specified here because django_assets tries to install Django>=1.7 and will
+    # force install Django2+ in setup
     setup_requires=[
         'django_assets >= 0.12',
+        'Django ~= 1.11.6',
     ],
     install_requires=[
         'django ~= 1.11.6',

src/edge/io.py

@@ -40,9 +40,10 @@ def to_gff_file(self, file):
                 # FeatureLocation first bp is AfterPosition, so -1
                 loc = FeatureLocation(annotation.base_first - 1, annotation.base_last)
                 qualifiers = {'name': annotation.feature.name}
+                strand = annotation.feature.strand
                 feature = SeqFeature(loc,
                                      type=annotation.feature.type,
-                                     strand=1,
+                                     strand=0 if strand is None else strand,
                                      qualifiers=qualifiers)
                 features.append(feature)
 

src/edge/tests/test_io.py

@@ -51,5 +51,29 @@ def test_outputs_gff(self):
 ##FASTA
 >Bar <unknown description>
 %s
+""" % (fragment.sequence,)
+        self.assertEquals(expected, gff)
+
+    def test_outputs_gff_handles_negative_strand(self):
+        fragment = self.fragment.indexed_fragment()
+        fragment.annotate(2, 9, 'A1', 'gene', -1)
+        fragment.insert_bases(3, 'gataca')
+
+        with tempfile.NamedTemporaryFile(mode='rw+', delete=False) as f:
+            f.close()
+            IO(self.genome).to_gff(f.name)
+            h = open(f.name, 'r')
+            gff = h.read()
+            h.close()
+            os.unlink(f.name)
+
+        # be aware of the tabs in the string below
+        expected = """##gff-version 3
+##sequence-region Bar 1 19
+Bar\tfeature\tgene\t2\t2\t.\t-\t.\tname=A1
+Bar\tfeature\tgene\t9\t15\t.\t-\t.\tname=A1
+##FASTA
+>Bar <unknown description>
+%s
 """ % (fragment.sequence,)
         self.assertEquals(expected, gff)