after fixing conflicts

fulcrumgenomics · Oct 7, 2024 · c0e869e · c0e869e
1 parent c3f0389
commit c0e869e
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Showing 2 changed files with 5 additions and 11 deletions.
diff --git a/prymer/primer3/primer3_input.py b/prymer/primer3/primer3_input.py
@@ -71,9 +71,9 @@
 PRIMER_MAX_POLY_X -> 5
 PRIMER_MAX_NS_ACCEPTED -> 1
 PRIMER_LOWERCASE_MASKING -> 1
+PRIMER_NUM_RETURN -> 5
 PRIMER_PAIR_WT_PRODUCT_SIZE_LT -> 1.0
 PRIMER_PAIR_WT_PRODUCT_SIZE_GT -> 1.0
-PRIMER_NUM_RETURN -> 5
 PRIMER_PAIR_WT_PRODUCT_TM_LT -> 0.0
 PRIMER_PAIR_WT_PRODUCT_TM_GT -> 0.0
 PRIMER_WT_END_STABILITY -> 0.25

diff --git a/prymer/primer3/primer3_weights.py b/prymer/primer3/primer3_weights.py
@@ -18,10 +18,9 @@
 
 Example:
 >>> PrimerAndAmpliconWeights() # default implementation
-PrimerAndAmpliconWeights(product_size_lt=1.0, product_size_gt=1, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0)
->>> PrimerAndAmpliconWeights(product_size_lt=5)
-PrimerAndAmpliconWeights(product_size_lt=5.0, product_size_gt=1, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0)
-
+PrimerAndAmpliconWeights(product_size_lt=1.0, product_size_gt=1.0, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0)
+>>> PrimerAndAmpliconWeights(product_size_lt=5.0)
+PrimerAndAmpliconWeights(product_size_lt=5.0, product_size_gt=1.0, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0)
 """  # noqa: E501
 
 from dataclasses import dataclass
@@ -56,12 +55,7 @@ class PrimerAndAmpliconWeights:
             `PrimerAndAmpliconParameters.primer_gcs.opt`
         primer_gc_gt: penalty weight for primers with GC percent higher than
             `PrimerAndAmpliconParameters.primer_gcs.opt`
-     Example:
-         >>> PrimerAndAmpliconWeights() #default implementation
-         Primer3Weights(product_size_lt=1.0, product_size_gt=1.0, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0)
-         >>> PrimerAndAmpliconWeights(product_size_lt=5.0)
-         Primer3Weights(product_size_lt=5.0, product_size_gt=1.0, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0)
-    """  # noqa: E501
+    """
 
     product_size_lt: float = 1.0
     product_size_gt: float = 1.0