diff --git a/prymer/primer3/primer3_input.py b/prymer/primer3/primer3_input.py index c6bea68..aaa29ca 100644 --- 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 index 55f7892..4668090 100644 --- 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