From de9df1fd0ff309cd18f31f348302a663efa8fdd0 Mon Sep 17 00:00:00 2001
From: Chris Mitchell <chris@ginkgobioworks.com>
Date: Tue, 12 Feb 2019 13:01:36 -0500
Subject: [PATCH 1/3] Fix export for negative strand

---
 src/edge/io.py            |  3 ++-
 src/edge/tests/test_io.py | 24 ++++++++++++++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/edge/io.py b/src/edge/io.py
index a9826450..e2b938cb 100644
--- a/src/edge/io.py
+++ b/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)
 
diff --git a/src/edge/tests/test_io.py b/src/edge/tests/test_io.py
index 80ef0d94..b01b5e89 100644
--- a/src/edge/tests/test_io.py
+++ b/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)

From f7db6d66809598ea27df5bc107131414964d0878 Mon Sep 17 00:00:00 2001
From: Chris Mitchell <chris@ginkgobioworks.com>
Date: Tue, 12 Feb 2019 13:50:43 -0500
Subject: [PATCH 2/3] Add django to setup.py setup_reqs

---
 setup.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/setup.py b/setup.py
index 3b05a042..014a5d48 100644
--- a/setup.py
+++ b/setup.py
@@ -126,6 +126,9 @@ def run(self):
 
     setup_requires=[
         'django_assets >= 0.12',
+         # This has to be installed here because django_assets tries to install Django>=1.7 and will
+         # force install Django2+ in setup
+        'Django ~= 1.11.6',
     ],
     install_requires=[
         'django ~= 1.11.6',

From 5ead19c98b5e6c51bb44bec1b4aaff13d8c8ec61 Mon Sep 17 00:00:00 2001
From: Chris Mitchell <chris@ginkgobioworks.com>
Date: Tue, 12 Feb 2019 14:17:48 -0500
Subject: [PATCH 3/3] Fix flake

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 014a5d48..e0c983c9 100644
--- a/setup.py
+++ b/setup.py
@@ -124,10 +124,10 @@ 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',
-         # This has to be installed here because django_assets tries to install Django>=1.7 and will
-         # force install Django2+ in setup
         'Django ~= 1.11.6',
     ],
     install_requires=[