added "possible overhangs feature"

goldenhinges/OverhangsSelector.py

@@ -36,6 +36,9 @@ class OverhangsSelector:
 
     forbidden_overhang
       List of all forbidden overhangs.
+    
+    possible_overhangs
+      List of a few overhangs the collection should be chosen from.
 
     time_limit
       Time in seconds after which the solvers should stop if no solution
@@ -46,7 +49,8 @@ class OverhangsSelector:
     """
 
     def __init__(self, gc_min=0, gc_max=1, differences=1, overhangs_size=4,
-                 forbidden_overhangs=(), forbidden_pairs=(), time_limit=None,
+                 forbidden_overhangs=(), forbidden_pairs=(),
+                 possible_overhangs=None, time_limit=None,
                  external_overhangs=(), progress_logger='bar'):
         """Initialize the object (see class description)."""
 
@@ -66,6 +70,9 @@ def progress_logger(**k):
         forbidden_overhangs = list(set(
             list(forbidden_overhangs) + [reverse_complement(o)
                                          for o in forbidden_overhangs]))
+        if possible_overhangs is not None:
+            forbidden_overhangs += [o for o in self.all_overhangs
+                                    if o not in possible_overhangs]
         for o1 in self.all_overhangs:
             reverse = reverse_complement(o1)
             if any([(sequences_differences(o1, o2) < self.differences) or

goldenhinges/reports.py

@@ -83,7 +83,7 @@ def write_report_for_cutting_solution(solution, target, sequence,
     ax.set_title("Selected overhangs", loc="left",
                  fontdict=dict(weight='bold', fontsize=13))
     ax.figure.set_size_inches((max(8, 0.7*len(o)), 2))
-    ax.set_ylim(ymax=ax.get_ylim()[1] + 2)
+    ax.set_ylim(top=ax.get_ylim()[1] + 2)
 
     xx = [x for (a, b) in edited_segments for x in range(a, b)]
     ax.plot(xx, [0 for x in xx], marker='o', c='r', lw=0,

setup.py

@@ -10,7 +10,7 @@
     version=__version__,
     author='Zulko',
     description='DNA overhangs design for Golden Gate etc.',
-    url='https://github.com/Edinburgh-Genome-Foundry/goldenhinges',
+    url='https://github.com/Edinburgh-Genome-Foundry/GoldenHinges',
     long_description=open('pypi-readme.rst').read(),
     license='see LICENSE.txt',
     keywords="DNA assembly overhangs constraint-programming synthetic-biology",

tests/test_basics.py

@@ -41,6 +41,14 @@ def test_generate_overhangs_collection2():
         assert sequences_differences(o1, o2) >= 2
         assert sequences_differences(o1, reverse_complement(o2)) >= 2
 
+def test_generate_overhangs_collection_with_possible():
+    selector = OverhangsSelector(gc_min=0.25, gc_max=0.75,
+                                 differences=1,
+                                 possible_overhangs=['ATTC', 'AAAA', 'GAAT',
+                                                     'CTCA'],
+                                 time_limit=2)
+    collection = selector.generate_overhangs_set()
+    assert len(collection) == 2
 
 def test_cut_sequence_into_similar_lengths(data):
     def invalid_overhang(overhang):