Merge pull request #82 from ondrej-sladky-eligo/master

All builtin specifications now correctly recognize `boost` parameter.

Author: veghp

dnachisel/builtin_specifications/AllowPrimer.py

@@ -62,19 +62,20 @@ def __init__(
         avoid_heterodim_with=None,
         max_heterodim_tm=5,
         avoided_repeats=((2, 5), (3, 4), (4, 3)),
+        boost=1.0,
     ):
         location = Location.from_data(location)
         specs = {
             "unique_sequence": UniquifyAllKmers(
-                k=max_homology_length, location=location
+                k=max_homology_length, location=location, boost=boost
             ),
             "melting_temperature": EnforceMeltingTemperature(
-                mini=tmin, maxi=tmax, location=location
+                mini=tmin, maxi=tmax, location=location, boost=boost
             ),
             **{
                 "repeats_%d_%d"
                 % (k, n): AvoidPattern(
-                    RepeatedKmerPattern(k, n), location=location
+                    RepeatedKmerPattern(k, n), location=location, boost=boost
                 )
                 for (k, n) in avoided_repeats
             },
@@ -84,5 +85,7 @@ def __init__(
                 other_primers_sequences=avoid_heterodim_with,
                 tmax=max_heterodim_tm,
                 location=location,
+                boost=boost,
             )
         self.register_specifications(specs)
+        self.boost = boost

dnachisel/builtin_specifications/AvoidBlastMatches.py

@@ -55,6 +55,7 @@ def __init__(
         e_value=1e80,
         culling_limit=1,
         location=None,
+        boost=1.0,
     ):
         """Initialize."""
         self.blast_db = blast_db
@@ -68,6 +69,7 @@ def __init__(
         self.e_value = e_value
         self.ungapped = ungapped
         self.culling_limit = culling_limit
+        self.boost = boost
 
     def initialized_on_problem(self, problem, role=None):
         return self._copy_with_full_span_if_no_location(problem)

dnachisel/builtin_specifications/AvoidHeterodimerization.py

@@ -36,6 +36,7 @@ def __init__(
         self.other_primers_sequences = other_primers_sequences
         self.tmax = tmax
         self.location = location
+        self.boost = boost
 
     def initialized_on_problem(self, problem, role=None):
         return self._copy_with_full_span_if_no_location(problem)

dnachisel/builtin_specifications/SequenceLengthBounds.py

@@ -20,9 +20,10 @@ class SequenceLengthBounds(Specification):
     """
     best_possible_score = 0
 
-    def __init__(self, min_length=0, max_length=None):
+    def __init__(self, min_length=0, max_length=None, boost=1.0):
         self.min_length = min_length
         self.max_length = max_length
+        self.boost = boost
 
     def evaluate(self, problem):
         """Return 0 if the sequence length is between the bounds, else -1"""

dnachisel/builtin_specifications/UniquifyAllKmers.py

@@ -137,7 +137,7 @@ def __init__(
             reference = Location.from_tuple(reference)
         self.reference = reference
         self.include_reverse_complement = include_reverse_complement
-        self.boost = 1.0
+        self.boost = boost
         self.localization_data = localization_data
 
     def initialized_on_problem(self, problem, role="constraint"):