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primer3_weights

Primer3Weights Class and Methods

The PrimerAndAmpliconWeights class holds the penalty weights that Primer3 uses to score primer designs.

The ProbeWeights class holds the penalty weights that Primer3 uses to score internal probe designs.

Primer3 considers the differential between user input (e.g., constraining the optimal primer size to be 18 bp) and the characteristics of a specific primer design (e.g., if the primer size is 19 bp). Depending on the "weight" of that characteristic, Primer3 uses an objective function to score a primer design and help define what an "optimal" design looks like.

By modifying these weights, users can prioritize specific primer design characteristics. Each of the defaults provided here are derived from the Primer3 manual: https://primer3.org/manual.html

Examples of interacting with the PrimerAndAmpliconWeights class

Example:

PrimerAndAmpliconWeights() # default implementation 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, primer_homodimer_wt=0.0, primer_3p_homodimer_wt=0.0, primer_secondary_structure_wt=0.0) 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, primer_homodimer_wt=0.0, primer_3p_homodimer_wt=0.0, primer_secondary_structure_wt=0.0)

Classes

PrimerAndAmpliconWeights dataclass

Holds the primer-specific weights that Primer3 uses to adjust design penalties.

The weights that Primer3 uses when a parameter is less than optimal are labeled with "_lt". "_gt" weights are penalties applied when a parameter is greater than optimal.

Some of these settings depart from the default settings enumerated in the Primer3 manual. Please see the Primer3 manual for additional details: https://primer3.org/manual.html#globalTags

Attributes:

Name Type Description
product_size_lt float

weight for products shorter than PrimerAndAmpliconParameters.amplicon_sizes.opt
product_size_gt float

weight for products longer than PrimerAndAmpliconParameters.amplicon_sizes.opt
product_tm_lt float

weight for products with a Tm lower than PrimerAndAmpliconParameters.amplicon_tms.opt
product_tm_gt float

weight for products with a Tm greater than PrimerAndAmpliconParameters.amplicon_tms.opt
primer_end_stability float

penalty for the calculated maximum stability for the last five 3' bases of primer
primer_gc_lt float

penalty for primers with GC percent lower than PrimerAndAmpliconParameters.primer_gcs.opt
primer_gc_gt float

weight for primers with GC percent higher than PrimerAndAmpliconParameters.primer_gcs.opt
primer_homodimer_wt float

penalty for the individual primer self binding value as specified in PrimerAndAmpliconParameters.primer_max_homodimer_tm
primer_3p_homodimer_wt float

weight for the 3'-anchored primer self binding value as specified in PrimerAndAmpliconParameters.primer_max_3p_homodimer_tm
primer_secondary_structure_wt float

penalty weight for the primer hairpin structure melting temperature as defined in PrimerAndAmpliconParameters.PRIMER_MAX_HAIRPIN_TH
Source code in prymer/primer3/primer3_weights.py 
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@dataclass(frozen=True, init=True, slots=True)
class PrimerAndAmpliconWeights:
    """Holds the primer-specific weights that Primer3 uses to adjust design penalties.

    The weights that Primer3 uses when a parameter is less than optimal are labeled with "_lt".
    "_gt" weights are penalties applied when a parameter is greater than optimal.

    Some of these settings depart from the default settings enumerated in the Primer3 manual.
    Please see the Primer3 manual for additional details:
        https://primer3.org/manual.html#globalTags

    Attributes:
        product_size_lt: weight for products shorter than
            `PrimerAndAmpliconParameters.amplicon_sizes.opt`
        product_size_gt: weight for products longer than
            `PrimerAndAmpliconParameters.amplicon_sizes.opt`
        product_tm_lt: weight for products with a Tm lower than
            `PrimerAndAmpliconParameters.amplicon_tms.opt`
        product_tm_gt: weight for products with a Tm greater than
            `PrimerAndAmpliconParameters.amplicon_tms.opt`
        primer_end_stability: penalty for the calculated maximum stability
            for the last five 3' bases of primer
        primer_gc_lt: penalty for primers with GC percent lower than
            `PrimerAndAmpliconParameters.primer_gcs.opt`
        primer_gc_gt: weight for primers with GC percent higher than
            `PrimerAndAmpliconParameters.primer_gcs.opt`
        primer_homodimer_wt: penalty for the individual primer self binding value as specified
            in `PrimerAndAmpliconParameters.primer_max_homodimer_tm`
        primer_3p_homodimer_wt: weight for the 3'-anchored primer self binding value as specified in
            `PrimerAndAmpliconParameters.primer_max_3p_homodimer_tm`
        primer_secondary_structure_wt: penalty weight for the primer hairpin structure melting
            temperature as defined in `PrimerAndAmpliconParameters.PRIMER_MAX_HAIRPIN_TH`

    """

    product_size_lt: float = 1.0
    product_size_gt: float = 1.0
    product_tm_lt: float = 0.0
    product_tm_gt: float = 0.0
    primer_end_stability: float = 0.25
    primer_gc_lt: float = 0.25
    primer_gc_gt: float = 0.25
    primer_self_any: float = 0.1
    primer_self_end: float = 0.1
    primer_size_lt: float = 0.5
    primer_size_gt: float = 0.1
    primer_tm_lt: float = 1.0
    primer_tm_gt: float = 1.0
    primer_homodimer_wt: float = 0.0
    primer_3p_homodimer_wt: float = 0.0
    primer_secondary_structure_wt: float = 0.0

    def to_input_tags(self) -> dict[Primer3InputTag, Any]:
        """Maps weights to Primer3InputTag to feed directly into Primer3."""
        mapped_dict = {
            Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_SIZE_LT: self.product_size_lt,
            Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_SIZE_GT: self.product_size_gt,
            Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_TM_LT: self.product_tm_lt,
            Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_TM_GT: self.product_tm_gt,
            Primer3InputTag.PRIMER_WT_END_STABILITY: self.primer_end_stability,
            Primer3InputTag.PRIMER_WT_GC_PERCENT_LT: self.primer_gc_lt,
            Primer3InputTag.PRIMER_WT_GC_PERCENT_GT: self.primer_gc_gt,
            Primer3InputTag.PRIMER_WT_SELF_ANY: self.primer_self_any,
            Primer3InputTag.PRIMER_WT_SELF_END: self.primer_self_end,
            Primer3InputTag.PRIMER_WT_SIZE_LT: self.primer_size_lt,
            Primer3InputTag.PRIMER_WT_SIZE_GT: self.primer_size_gt,
            Primer3InputTag.PRIMER_WT_TM_LT: self.primer_tm_lt,
            Primer3InputTag.PRIMER_WT_TM_GT: self.primer_tm_gt,
            Primer3InputTag.PRIMER_WT_SELF_ANY_TH: self.primer_homodimer_wt,
            Primer3InputTag.PRIMER_WT_SELF_END_TH: self.primer_3p_homodimer_wt,
            Primer3InputTag.PRIMER_WT_HAIRPIN_TH: self.primer_secondary_structure_wt,
        }
        return mapped_dict

Functions

to_input_tags 
to_input_tags() -> dict[Primer3InputTag, Any]

Maps weights to Primer3InputTag to feed directly into Primer3.

Source code in prymer/primer3/primer3_weights.py 
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def to_input_tags(self) -> dict[Primer3InputTag, Any]:
    """Maps weights to Primer3InputTag to feed directly into Primer3."""
    mapped_dict = {
        Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_SIZE_LT: self.product_size_lt,
        Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_SIZE_GT: self.product_size_gt,
        Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_TM_LT: self.product_tm_lt,
        Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_TM_GT: self.product_tm_gt,
        Primer3InputTag.PRIMER_WT_END_STABILITY: self.primer_end_stability,
        Primer3InputTag.PRIMER_WT_GC_PERCENT_LT: self.primer_gc_lt,
        Primer3InputTag.PRIMER_WT_GC_PERCENT_GT: self.primer_gc_gt,
        Primer3InputTag.PRIMER_WT_SELF_ANY: self.primer_self_any,
        Primer3InputTag.PRIMER_WT_SELF_END: self.primer_self_end,
        Primer3InputTag.PRIMER_WT_SIZE_LT: self.primer_size_lt,
        Primer3InputTag.PRIMER_WT_SIZE_GT: self.primer_size_gt,
        Primer3InputTag.PRIMER_WT_TM_LT: self.primer_tm_lt,
        Primer3InputTag.PRIMER_WT_TM_GT: self.primer_tm_gt,
        Primer3InputTag.PRIMER_WT_SELF_ANY_TH: self.primer_homodimer_wt,
        Primer3InputTag.PRIMER_WT_SELF_END_TH: self.primer_3p_homodimer_wt,
        Primer3InputTag.PRIMER_WT_HAIRPIN_TH: self.primer_secondary_structure_wt,
    }
    return mapped_dict

ProbeWeights dataclass

Holds the probe-specific weights that Primer3 uses to adjust design penalties.

Attributes:

Name Type Description
probe_size_lt float

penalty for probes shorter than ProbeParameters.probe_sizes.opt
probe_size_gt float

penalty for probes longer than ProbeParameters.probe_sizes.opt
probe_tm_lt float

penalty for probes with a Tm lower than ProbeParameters.probe_tms.opt
probe_tm_gt float

penalty for probes with a Tm greater than ProbeParameters.probe_tms.opt
probe_gc_lt float

penalty for probes with GC content lower than ProbeParameters.probe_gcs.opt
probe_gc_gt float

penalty for probes with GC content greater than ProbeParameters.probe_gcs.opt
probe_wt_self_any_th float

penalty for probe self-complementarity as defined in ProbeParameters.probe_max_self_any_thermo
probe_wt_self_end float

penalty for probe 3' complementarity as defined in ProbeParameters.probe_max_self_end_thermo
probe_wt_hairpin_th float

penalty for the most stable primer hairpin structure value as defined in ProbeParameters.probe_max_hairpin_thermo

Each of these defaults are taken from the Primer3 manual. More details can be found here: https://primer3.org/manual.html

Source code in prymer/primer3/primer3_weights.py 
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@dataclass(frozen=True, init=True, slots=True)
class ProbeWeights:
    """Holds the probe-specific weights that Primer3 uses to adjust design penalties.

    Attributes:
        probe_size_lt: penalty for probes shorter than `ProbeParameters.probe_sizes.opt`
        probe_size_gt: penalty for probes longer than `ProbeParameters.probe_sizes.opt`
        probe_tm_lt: penalty for probes with a Tm lower than `ProbeParameters.probe_tms.opt`
        probe_tm_gt: penalty for probes with a Tm greater than `ProbeParameters.probe_tms.opt`
        probe_gc_lt: penalty for probes with GC content lower than `ProbeParameters.probe_gcs.opt`
        probe_gc_gt: penalty for probes with GC content greater than `ProbeParameters.probe_gcs.opt`
        probe_wt_self_any_th: penalty for probe self-complementarity as defined in
            `ProbeParameters.probe_max_self_any_thermo`
        probe_wt_self_end: penalty for probe 3' complementarity as defined in
            `ProbeParameters.probe_max_self_end_thermo`
        probe_wt_hairpin_th: penalty for the most stable primer hairpin structure value as defined
            in `ProbeParameters.probe_max_hairpin_thermo`

    Each of these defaults are taken from the Primer3 manual. More details can be found here:
    https://primer3.org/manual.html

    """

    probe_size_lt: float = 1.0
    probe_size_gt: float = 1.0
    probe_tm_lt: float = 1.0
    probe_tm_gt: float = 1.0
    probe_gc_lt: float = 0.0
    probe_gc_gt: float = 0.0
    probe_homodimer_wt: float = 0.0
    probe_3p_homodimer_wt: float = 0.0
    probe_secondary_structure_wt: float = 0.0

    def to_input_tags(self) -> dict[Primer3InputTag, Any]:
        """Maps weights to Primer3InputTag to feed directly into Primer3."""
        mapped_dict = {
            Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_LT: self.probe_size_lt,
            Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_GT: self.probe_size_gt,
            Primer3InputTag.PRIMER_INTERNAL_WT_TM_LT: self.probe_tm_lt,
            Primer3InputTag.PRIMER_INTERNAL_WT_TM_GT: self.probe_tm_gt,
            Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_LT: self.probe_gc_lt,
            Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_GT: self.probe_gc_gt,
            Primer3InputTag.PRIMER_INTERNAL_WT_SELF_ANY_TH: self.probe_homodimer_wt,
            Primer3InputTag.PRIMER_INTERNAL_WT_SELF_END_TH: self.probe_3p_homodimer_wt,
            Primer3InputTag.PRIMER_INTERNAL_WT_HAIRPIN_TH: self.probe_secondary_structure_wt,
        }
        return mapped_dict

Functions

to_input_tags 
to_input_tags() -> dict[Primer3InputTag, Any]

Maps weights to Primer3InputTag to feed directly into Primer3.

Source code in prymer/primer3/primer3_weights.py 
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def to_input_tags(self) -> dict[Primer3InputTag, Any]:
    """Maps weights to Primer3InputTag to feed directly into Primer3."""
    mapped_dict = {
        Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_LT: self.probe_size_lt,
        Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_GT: self.probe_size_gt,
        Primer3InputTag.PRIMER_INTERNAL_WT_TM_LT: self.probe_tm_lt,
        Primer3InputTag.PRIMER_INTERNAL_WT_TM_GT: self.probe_tm_gt,
        Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_LT: self.probe_gc_lt,
        Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_GT: self.probe_gc_gt,
        Primer3InputTag.PRIMER_INTERNAL_WT_SELF_ANY_TH: self.probe_homodimer_wt,
        Primer3InputTag.PRIMER_INTERNAL_WT_SELF_END_TH: self.probe_3p_homodimer_wt,
        Primer3InputTag.PRIMER_INTERNAL_WT_HAIRPIN_TH: self.probe_secondary_structure_wt,
    }
    return mapped_dict