API Reference¶

Design¶

Core design modules.

For examples for how to use the design module, see the Usage Docs For a list of design parameters available, take a look at the BoulderIO Parameters

# a new task
design = Design()

# set template sequence
design.settings.template("AGGTTGCGTGTGTATGGTCGTGTAGTGTGT")

# set left primer sequence
design.settings.left_sequence("GTTGCGTGTGT)

# set as a cloning task
design.settings.as_cloning_task()

# run the design task
design.run()

class primer3plus.design.Design[source]¶

Initialize a new design. Set parameters using.

Design.settings, which returns an instance of DesignPresets.

Alternatively, parameters can be accessed more directly using the name of the parameter descriptor. For a list of parameters available, see BoulderIO Parameters.

design = Design()
design.settings.template("AGGCTGTAGTGCTTGTAGCTGGTTGCGTTACTGTG")
design.settings.left_sequence("GTAGTGCTTGTA")
design.SEQUENCE_ID.value = "MY ID"
design.run()

run()[source]¶

Design primers. Optionally provide additional parameters.

Parameters: params –
Return type: Tuple[List[Dict], List[Dict]]
Returns: results

run_and_optimize(max_iterations, params=None, gradient=None, pick_anyway=False)[source]¶

Design primers. If primer design is unsuccessful, relax parameters as defined in primer3plust.Design.DEFAULT_GRADIENT. Repeat for the specified number of max_iterations.

Parameters

max_iterations – the max number of iterations to perform relaxation
params (Optional[BoulderIO]) – optional parameters to provide
gradient (Optional[Dict[str, Tuple[Union[float, int], Union[float, int], Union[float, int]]]]) – optional gradient to provide. If not provided, Design.DEFAULT_GRADIENT will be used. The gradient is a dictionary off 3 tuples, the step the min and the max.
pick_anyway (bool) – if set to True, if the optimization finds no pairs, pick a pair anyways.

Return type

Tuple[List[dict], List[dict]]

Returns

results

property settings¶

Return the DesignPresets instance for this design.

Return type: DesignPresets

update(data)[source]¶: Update an arbitrary parameter.

class primer3plus.design.DesignBase(gradient=None, params=None, quiet_runtime=False)[source]¶

Base design.

Initializes a new design.

Parameters

gradient (Optional[Dict[str, Tuple[Union[float, int], Union[float, int], Union[float, int]]]]) – the design gradient.
quiet_runtime (bool) – if True will siliently ignore any runtime errors.

DEFAULT_GRADIENT = {'PRIMER_MAX_HAIRPIN_TH': (1, 47.0, 60), 'PRIMER_MAX_SIZE': (1, 27, 36), 'PRIMER_MAX_TM': (1, 27, 80), 'PRIMER_MIN_SIZE': (-1, 16, 27), 'PRIMER_MIN_TM': (-1, 48, 57.0)}¶: the default gradient to use for the Design.run_and_optimize() method.

DEFAULT_PARAMS = <primer3plus.params.BoulderIO object>¶: default parameters

copy()[source]¶: Copy this design and its parameters.

static open_help()[source]¶: Open the documentation help in a new browser tab.

run()[source]¶

Design primers. Optionally provide additional parameters.

Parameters: params –
Return type: Tuple[List[Dict], List[Dict]]
Returns: results

run_and_optimize(max_iterations, params=None, gradient=None, run_kwargs=None)[source]¶

Design primers and relax constraints. If primer design is unsuccessful, relax parameters as defined in primer3plust.Design.DEFAULT_GRADIENT. Repeat for the specified number of max_iterations.

Parameters

max_iterations – the max number of iterations to perform relaxation
params (Optional[BoulderIO]) – optional parameters to provide
gradient (Optional[Dict[str, Tuple[Union[float, int], Union[float, int], Union[float, int]]]]) – optional gradient to provide. If not provided, Design.DEFAULT_GRADIENT will be used. The gradient is a dictionary off 3 tuples, the step the min and the max.

Return type

Tuple[List[dict], List[dict]]

Returns

results

class primer3plus.design.DesignPresets(design)[source]¶

Interface for setting design parameters. This is typically accessed from a Design instance’s.

Design method. As in:

design = Design()
design.settings.left_sequence("AGGGAGATAGATA")
design.run()

Initializes a new interface from a.

Design.

Parameters: design – The design

as_cloning_task()[source]¶

Set the design as a cloning task.

http://primer3.ut.ee/primer3web_help.htm#PRIMER_TASK

Return type: DesignPresets
Returns: self

as_generic_task()[source]¶

Set the design as a generic task.

http://primer3.ut.ee/primer3web_help.htm#PRIMER_TASK

Return type: DesignPresets
Returns: self

excluded(interval)[source]¶

Primers and oligos may not overlap any region specified in this tag. The associated value must be a space-separated list of <start>,<length> pairs where <start> is the index of the first base of the excluded region, and <length> is its length. This tag is useful for tasks such as excluding regions of low sequence quality or for excluding regions containing repetitive elements such as ALUs or LINEs.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_TEMPLATE http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_EXCLUDED_REGION

Parameters: interval (Union[str, Tuple[int, int], List[Tuple[int, int]]]) – One of the following: the sequence of the target region, a tuple of the interval of <start>,<length>, or a list of tuples of <start>,<length>
Return type: DesignPresets
Returns: self

included(interval)[source]¶

Specify interval from which primers must be selected. A sub-region of the given sequence in which to pick primers. For example, often the first dozen or so bases of a sequence are vector, and should be excluded from consideration. The value for this parameter has the form.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_INCLUDED_REGION

<start>,<length> where <start> is the index of the first base to consider, and <length> is the number of subsequent bases in the primer-picking region.

Parameters: interval (Union[str, Tuple[int, int]]) – One of the following: the sequence of the target region, a tuple of the interval of <start>,<length> or a str
Return type: DesignPresets
Returns: self

internal_sequence(primer)[source]¶

The sequence of an internal oligo to check and around which to design left and right primers. Must be a substring of SEQUENCE_TEMPLATE.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_INTERNAL_OLIGO http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_INTERNAL_OLIGO

Parameters

primer (str) –

type primer

return

rtype

Return type

DesignPresets

left_overhang(overhang)[source]¶

Sets the left overhang sequence for the primer. This overhang will.

always be in the overhang sequence regardless of other parameters.

If using a primer that anneals with an overhang, this value will be appended to the 5’ end of the overhang.

Parameters: overhang (str) – overhang sequence
Return type: DesignPresets
Returns: self

left_sequence(primer)[source]¶

The sequence of a left primer to check and around which to design right primers and optional internal oligos. Must be a substring of SEQUENCE_TEMPLATE.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_PRIMER http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_RIGHT_PRIMER

Parameters: primer (str) – the primer sequence
Return type: DesignPresets
Returns: self

long_ok(b=True)[source]¶

Set the BoulderIO to process long primers.

Parameters: b (bool) – boolean to set
Return type: DesignPresets
Returns: self

pair_region_list(region_list)[source]¶

The list of regions from which to design primers.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_PRIMER_PAIR_OK_REGION_LIST

Parameters: region_list (List[Tuple[int, int, int, int]]) – list of regions
Return type: DesignPresets
Returns: self

pick_anyway(b=1)[source]¶

If true use primer provided in SEQUENCE_PRIMER, SEQUENCE_PRIMER_REVCOMP, or SEQUENCE_INTERNAL_OLIGO even if it violates specific constraints.

http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_ANYWAY

Parameters: b – default True

:return self

Return type: DesignPresets

pick_left_only()[source]¶

Design only the left primer.

http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_LEFT_PRIMER http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_RIGHT_PRIMER

Return type: DesignPresets
Returns: self

pick_right_only()[source]¶

Design only the right primer.

http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_LEFT_PRIMER http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_RIGHT_PRIMER

Return type: DesignPresets
Returns: self

primer_num_return(n)[source]¶

Set the number of primers to return for the design task.

http://primer3.ut.ee/primer3web_help.htm#PRIMER_NUM_RETURN

Parameters: n (int) – number of primers to return
Return type: DesignPresets
Returns: self

primers(p1, p2)[source]¶

Set the left and right primer sequences.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_PRIMER http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_RIGHT_PRIMER http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_PRIMER_REVCOMP http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_LEFT_PRIMER

Parameters

p1 (str) –
p2 (str) –

Return type

DesignPresets

Returns

product_size(interval, opt=None)[source]¶

Set the product size. Optionally include the optimal size.

http://primer3.ut.ee/primer3web_help.htm#PRIMER_PRODUCT_SIZE_RANGE http://primer3.ut.ee/primer3web_help.htm#PRIMER_PRODUCT_OPT_SIZE

Parameters

interval (Union[Tuple[int, int], List[Tuple[int, int]]]) – a tuple of <min>,<max> or a list of such tuples
opt – optional product size as an int.

Return type

DesignPresets

Returns

self

right_overhang(overhang)[source]¶

Sets the right overhang sequence for the primer. This overhang will.

always be in the overhang sequence regardless of other parameters.

If using a primer that anneals with an overhang, this value will be appended to the 5’ end of the overhang.

Parameters: overhang (str) – overhang sequence
Return type: DesignPresets
Returns: self

right_sequence(primer)[source]¶

The sequence of a right primer to check and around which to design left primers and optional internal oligos. Must be a substring of the reverse strand of SEQUENCE_TEMPLATE.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_PRIMER_REVCOMP http://primer3.ut.ee/primer3web_help.htm#PRIMER_PICK_LEFT_PRIMER

Parameters: primer (str) – the primer sequence
Return type: DesignPresets
Returns: self

target(interval)[source]¶

Specify the interval that designed primers must flank. If one or more targets is specified then a legal primer pair must flank at least one of them. A target might be a simple sequence repeat site (for example a CA repeat) or a single-base-pair polymorphism, or an exon for resequencing. The value should be a space-separated list of.

<start>,<length> pairs where <start> is the index of the first base of a target,and <length> is its length. See also PRIMER_INSIDE_PENALTY, PRIMER_OUTSIDE_PENALTY. PRIMER_TASK=pick_sequencing_primers. See PRIMER_TASK for more information.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_TEMPLATE http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_TARGET

Parameters: interval (Union[str, Tuple[int, int], List[Tuple[int, int]]]) – One of the following: the sequence of the target region, a tuple of the interval of <start>,<length>, or a list of tuples of <start>,<length>

:return self

Return type: DesignPresets

task(task)[source]¶

This tag tells primer3 what task to perform.

http://primer3.ut.ee/primer3web_help.htm#PRIMER_TASK

Parameters: task (str) – the task name

:return self

Return type: DesignPresets

template(template)[source]¶

Set the template sequence for the design. This sets the ‘SEQUENCE_TEMPLATE’ parameter.

http://primer3.ut.ee/primer3web_help.htm#SEQUENCE_TEMPLATE

Parameters: template (str) – the template sequence
Return type: DesignPresets
Returns: self

update(update)[source]¶: Update an arbitrary parameter.

use_overhangs(b=True)[source]¶

Set the BoulderIO to process overhangs.

Parameters: b (bool) – boolean to set :return: self
Return type: DesignPresets

class primer3plus.design.RestoreAfterRun(boulderio)[source]¶: Class to restore boulderio to its original parameters after a run.

primer3plus.design.new(params=None)[source]¶: Start a new design.

Parameter Interface¶

Design Parameters¶

class primer3plus.params.BoulderIO[source]¶

Class that maintains and validates a list of Primer3 parameters.

Initializes a new BoulderIO instance.

EXTRA_TYPES = [<ParameterType SEQUENCE_PRIMER_OVERHANG <class 'str'> default=>, <ParameterType SEQUENCE_PRIMER_REVCOMP_OVERHANG <class 'str'> default=>, <ParameterType PRIMER_USE_OVERHANGS <class 'bool'> default=False>, <ParameterType PRIMER_LONG_OK <class 'bool'> default=False>, <ParameterType PRIMER_MIN_ANNEAL_CHECK <class 'int'> default=12>, <ParameterType _SEQUENCE_LONG_OVERHANG <class 'str'> default=>, <ParameterType _SEQUENCE_REVCOMP_LONG_OVERHANG <class 'str'> default=>]¶: extra parameter types

PRIMER_MAX_SIZE_HARD_LIM = 35¶: hard coded primer length limit for Primer3.

items() → a set-like object providing a view on D’s items[source]¶

load(param_dict)[source]¶

Load parameters from a dictionary.

Parameters: param_dict –
Returns

static online_help(open=False, key=None)[source]¶

Display online help in a browser tab.

Parameters

open – if True, open browser tab. Else return url.
key – optional parameter key

Return type

str

Returns

set_defaults()[source]¶

Set all parameters to their defaults.

Returns

update(data_dict)[source]¶

Update the parameters from a dictionary of key:values.

Parameters: data_dict (Dict[str, Any]) – update dictionary
Returns: None

values()[source]¶

Iterator for parameter values.

Return type: Iterator[Any]
Returns: iterator over parameter values

class primer3plus.params.ParamParser[source]¶

Reads the Primer3 documentation and creates the appropriate parameters.

classmethod open(filepath=None)[source]¶

Open the parameters from the filepath.

Parameters: filepath – filepath
Return type: BoulderIO
Returns

class primer3plus.params.ParamTypes[source]¶

Parameter types used in BoulderIO.

Only the Global and Sequence parameters are actually used in designs.

CATEGORY = 'category'¶: boulderIO that gets sent to primer3

EXTRA = 'extra'¶: extra parameter key. These do not show up in the final

GLOBAL = 'GLOBAL'¶: global parameter key

OTHER = 'OTHER'¶: other parameter key

PROGRAM = 'PROGRAM'¶: program parameter key

SEQUENCE = 'SEQUENCE'¶: sequence parameter key

class primer3plus.params.Parameter(ptype, value=None, restore=None)[source]¶

An instance of a Primer3 parameter.

Internally validate its value using its :class:<ParameterType <primer3plus.params.ParameterType>`

Initialize a parameter from a.

Parameter

Parameters

ptype (ParameterType) – parameter type
value – value to set parameter
restore (Optional[Any]) – optional restoration value

copy()[source]¶

Make a copy of this parameter.

Return type: Parameter
Returns: None

hold_restore()[source]¶

Hold current value for later restoration.

Returns

property name¶

Return the name of the parameter.

Returns: parameter name

restore()[source]¶

Restores the parameter to some original value.

Returns

set_default()[source]¶

Set the parameter to its default.

Returns: None

property value¶

Return the value of the parameter.

Return type: Any
Returns: Any

class primer3plus.params.ParameterType(name, description, type, default, category)[source]¶

Metatype for a Primer3 parameter.

Initialize a BoulderIO parameter type.

Parameters

name – name of the parameter
description – description of the parameter
type – expected type of the parameter
default – default value of the parameter
category – parameter category (from ‘sequence’, ‘program’, ‘globals’, or ‘other’)

category¶: category. See ParamTypes

default¶: default value

description¶: parameter description as a str

name¶: name of the parameter

type¶: expected python type of the parameter value

primer3plus.params.default_boulderio = <primer3plus.params.BoulderIO object>¶: default boulder IO parameters

BoulderIO Default Parameters¶

Default¶
name	type	value
SEQUENCE_ID	<class ‘str’>
SEQUENCE_TEMPLATE	<class ‘str’>
SEQUENCE_INCLUDED_REGION	<class ‘list’>	[]
SEQUENCE_TARGET	<class ‘list’>	[]
SEQUENCE_EXCLUDED_REGION	<class ‘list’>	[]
SEQUENCE_PRIMER_PAIR_OK_REGION_LIST	<class ‘list’>	[]
SEQUENCE_OVERLAP_JUNCTION_LIST	<class ‘list’>	[]
SEQUENCE_INTERNAL_EXCLUDED_REGION	<class ‘list’>	[]
SEQUENCE_PRIMER	<class ‘str’>
SEQUENCE_INTERNAL_OLIGO	<class ‘str’>
SEQUENCE_PRIMER_REVCOMP	<class ‘str’>
SEQUENCE_START_CODON_POSITION	<class ‘int’>	-2000000
SEQUENCE_QUALITY	<class ‘list’>	[]
SEQUENCE_FORCE_LEFT_START	<class ‘int’>	-1000000
SEQUENCE_FORCE_LEFT_END	<class ‘int’>	-1000000
SEQUENCE_FORCE_RIGHT_START	<class ‘int’>	-1000000
SEQUENCE_FORCE_RIGHT_END	<class ‘int’>	-1000000
PRIMER_TASK	<class ‘str’>	generic
PRIMER_PICK_LEFT_PRIMER	<class ‘bool’>	True
PRIMER_PICK_INTERNAL_OLIGO	<class ‘bool’>	False
PRIMER_PICK_RIGHT_PRIMER	<class ‘bool’>	True
PRIMER_NUM_RETURN	<class ‘int’>	5
PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION	<class ‘int’>	4
PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION	<class ‘int’>	7
PRIMER_MUST_MATCH_FIVE_PRIME	<class ‘str’>
PRIMER_INTERNAL_MUST_MATCH_FIVE_PRIME	<class ‘str’>
PRIMER_MUST_MATCH_THREE_PRIME	<class ‘str’>
PRIMER_INTERNAL_MUST_MATCH_THREE_PRIME	<class ‘str’>
PRIMER_PRODUCT_SIZE_RANGE	<class ‘list’>	[100, 300]
PRIMER_PRODUCT_OPT_SIZE	<class ‘int’>	0
PRIMER_PAIR_WT_PRODUCT_SIZE_LT	<class ‘float’>	0.0
PRIMER_PAIR_WT_PRODUCT_SIZE_GT	<class ‘float’>	0.0
PRIMER_MIN_SIZE	<class ‘int’>	18
PRIMER_INTERNAL_MIN_SIZE	<class ‘int’>	18
PRIMER_OPT_SIZE	<class ‘int’>	20
PRIMER_INTERNAL_OPT_SIZE	<class ‘int’>	20
PRIMER_MAX_SIZE	<class ‘int’>	27
PRIMER_INTERNAL_MAX_SIZE	<class ‘int’>	27
PRIMER_WT_SIZE_LT	<class ‘float’>	1.0
PRIMER_INTERNAL_WT_SIZE_LT	<class ‘float’>	1.0
PRIMER_WT_SIZE_GT	<class ‘float’>	1.0
PRIMER_INTERNAL_WT_SIZE_GT	<class ‘float’>	1.0
PRIMER_MIN_GC	<class ‘float’>	20.0
PRIMER_INTERNAL_MIN_GC	<class ‘float’>	20.0
PRIMER_OPT_GC_PERCENT	<class ‘float’>	50.0
PRIMER_INTERNAL_OPT_GC_PERCENT	<class ‘float’>	50.0
PRIMER_MAX_GC	<class ‘float’>	80.0
PRIMER_INTERNAL_MAX_GC	<class ‘float’>	80.0
PRIMER_WT_GC_PERCENT_LT	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_GC_PERCENT_LT	<class ‘float’>	0.0
PRIMER_WT_GC_PERCENT_GT	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_GC_PERCENT_GT	<class ‘float’>	0.0
PRIMER_GC_CLAMP	<class ‘int’>	0
PRIMER_MAX_END_GC	<class ‘int’>	5
PRIMER_MIN_TM	<class ‘float’>	57.0
PRIMER_INTERNAL_MIN_TM	<class ‘float’>	57.0
PRIMER_OPT_TM	<class ‘float’>	60.0
PRIMER_INTERNAL_OPT_TM	<class ‘float’>	60.0
PRIMER_MAX_TM	<class ‘float’>	63.0
PRIMER_INTERNAL_MAX_TM	<class ‘float’>	63.0
PRIMER_PAIR_MAX_DIFF_TM	<class ‘float’>	100.0
PRIMER_WT_TM_LT	<class ‘float’>	1.0
PRIMER_INTERNAL_WT_TM_LT	<class ‘float’>	1.0
PRIMER_WT_TM_GT	<class ‘float’>	1.0
PRIMER_INTERNAL_WT_TM_GT	<class ‘float’>	1.0
PRIMER_PAIR_WT_DIFF_TM	<class ‘float’>	0.0
PRIMER_PRODUCT_MIN_TM	<class ‘float’>	-1000000.0
PRIMER_PRODUCT_OPT_TM	<class ‘float’>	0.0
PRIMER_PRODUCT_MAX_TM	<class ‘float’>	1000000.0
PRIMER_PAIR_WT_PRODUCT_TM_LT	<class ‘float’>	0.0
PRIMER_PAIR_WT_PRODUCT_TM_GT	<class ‘float’>	0.0
PRIMER_TM_FORMULA	<class ‘int’>	1
PRIMER_SALT_MONOVALENT	<class ‘float’>	50.0
PRIMER_INTERNAL_SALT_MONOVALENT	<class ‘float’>	50.0
PRIMER_SALT_DIVALENT	<class ‘float’>	1.5
PRIMER_INTERNAL_SALT_DIVALENT	<class ‘float’>	0.0
PRIMER_DNTP_CONC	<class ‘float’>	0.6
PRIMER_INTERNAL_DNTP_CONC	<class ‘float’>	0.0
PRIMER_SALT_CORRECTIONS	<class ‘int’>	1
PRIMER_DNA_CONC	<class ‘float’>	50.0
PRIMER_INTERNAL_DNA_CONC	<class ‘float’>	50.0
PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT	<class ‘bool’>	True
PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT	<class ‘bool’>	False
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT	<class ‘bool’>	False
PRIMER_THERMODYNAMIC_PARAMETERS_PATH	<class ‘str’>	./primer3_config
PRIMER_MAX_SELF_ANY	<class ‘float’>	8.0
PRIMER_MAX_SELF_ANY_TH	<class ‘float’>	47.0
PRIMER_INTERNAL_MAX_SELF_ANY	<class ‘float’>	12.0
PRIMER_INTERNAL_MAX_SELF_ANY_TH	<class ‘float’>	47.0
PRIMER_PAIR_MAX_COMPL_ANY	<class ‘float’>	8.0
PRIMER_PAIR_MAX_COMPL_ANY_TH	<class ‘float’>	47.0
PRIMER_WT_SELF_ANY	<class ‘float’>	0.0
PRIMER_WT_SELF_ANY_TH	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_SELF_ANY	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_SELF_ANY_TH	<class ‘float’>	0.0
PRIMER_PAIR_WT_COMPL_ANY	<class ‘float’>	0.0
PRIMER_PAIR_WT_COMPL_ANY_TH	<class ‘float’>	0.0
PRIMER_MAX_SELF_END	<class ‘float’>	3.0
PRIMER_MAX_SELF_END_TH	<class ‘float’>	47.0
PRIMER_INTERNAL_MAX_SELF_END	<class ‘float’>	12.0
PRIMER_INTERNAL_MAX_SELF_END_TH	<class ‘float’>	47.0
PRIMER_PAIR_MAX_COMPL_END	<class ‘float’>	3.0
PRIMER_PAIR_MAX_COMPL_END_TH	<class ‘float’>	47.0
PRIMER_WT_SELF_END	<class ‘float’>	0.0
PRIMER_WT_SELF_END_TH	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_SELF_END	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_SELF_END_TH	<class ‘float’>	0.0
PRIMER_PAIR_WT_COMPL_END	<class ‘float’>	0.0
PRIMER_PAIR_WT_COMPL_END_TH	<class ‘float’>	0.0
PRIMER_MAX_HAIRPIN_TH	<class ‘float’>	47.0
PRIMER_INTERNAL_MAX_HAIRPIN_TH	<class ‘float’>	47.0
PRIMER_WT_HAIRPIN_TH	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_HAIRPIN_TH	<class ‘float’>	0.0
PRIMER_MAX_END_STABILITY	<class ‘float’>	100.0
PRIMER_WT_END_STABILITY	<class ‘float’>	0.0
PRIMER_MAX_NS_ACCEPTED	<class ‘int’>	0
PRIMER_INTERNAL_MAX_NS_ACCEPTED	<class ‘int’>	0
PRIMER_WT_NUM_NS	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_NUM_NS	<class ‘float’>	0.0
PRIMER_MAX_POLY_X	<class ‘int’>	5
PRIMER_INTERNAL_MAX_POLY_X	<class ‘int’>	5
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE	<class ‘int’>	-1
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE	<class ‘int’>	-1
PRIMER_MIN_THREE_PRIME_DISTANCE	<class ‘int’>	-1
PRIMER_PICK_ANYWAY	<class ‘bool’>	False
PRIMER_LOWERCASE_MASKING	<class ‘int’>	0
PRIMER_EXPLAIN_FLAG	<class ‘bool’>	True
PRIMER_LIBERAL_BASE	<class ‘bool’>	False
PRIMER_FIRST_BASE_INDEX	<class ‘int’>	0
PRIMER_MAX_TEMPLATE_MISPRIMING	<class ‘float’>	-1.0
PRIMER_MAX_TEMPLATE_MISPRIMING_TH	<class ‘float’>	-1.0
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING	<class ‘float’>	-1.0
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH	<class ‘float’>	-1.0
PRIMER_WT_TEMPLATE_MISPRIMING	<class ‘float’>	0.0
PRIMER_WT_TEMPLATE_MISPRIMING_TH	<class ‘float’>	0.0
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING	<class ‘float’>	0.0
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING_TH	<class ‘float’>	0.0
PRIMER_MISPRIMING_LIBRARY	<class ‘str’>
PRIMER_INTERNAL_MISHYB_LIBRARY	<class ‘str’>
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS	<class ‘bool’>	False
PRIMER_MAX_LIBRARY_MISPRIMING	<class ‘float’>	12.0
PRIMER_INTERNAL_MAX_LIBRARY_MISHYB	<class ‘float’>	12.0
PRIMER_PAIR_MAX_LIBRARY_MISPRIMING	<class ‘float’>	24.0
PRIMER_WT_LIBRARY_MISPRIMING	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_LIBRARY_MISHYB	<class ‘float’>	0.0
PRIMER_PAIR_WT_LIBRARY_MISPRIMING	<class ‘float’>	0.0
PRIMER_MASK_TEMPLATE	<class ‘bool’>	False
PRIMER_MASK_FAILURE_RATE	<class ‘float’>	0.1
PRIMER_WT_MASK_FAILURE_RATE	<class ‘float’>	0.0
PRIMER_MASK_5P_DIRECTION	<class ‘int’>	1
PRIMER_MASK_3P_DIRECTION	<class ‘int’>	0
PRIMER_MASK_KMERLIST_PATH	<class ‘str’>	../kmer_lists/
PRIMER_MASK_KMERLIST_PREFIX	<class ‘str’>	homo_sapiens
PRIMER_MIN_QUALITY	<class ‘int’>	0
PRIMER_INTERNAL_MIN_QUALITY	<class ‘int’>	0
PRIMER_MIN_END_QUALITY	<class ‘int’>	0
PRIMER_QUALITY_RANGE_MIN	<class ‘int’>	0
PRIMER_QUALITY_RANGE_MAX	<class ‘int’>	100
PRIMER_WT_SEQ_QUAL	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_SEQ_QUAL	<class ‘float’>	0.0
PRIMER_PAIR_WT_PR_PENALTY	<class ‘float’>	1.0
PRIMER_PAIR_WT_IO_PENALTY	<class ‘float’>	0.0
PRIMER_INSIDE_PENALTY	<class ‘float’>	-1.0
PRIMER_OUTSIDE_PENALTY	<class ‘float’>	0.0
PRIMER_WT_POS_PENALTY	<class ‘float’>	1.0
PRIMER_SEQUENCING_LEAD	<class ‘int’>	50
PRIMER_SEQUENCING_SPACING	<class ‘int’>	500
PRIMER_SEQUENCING_INTERVAL	<class ‘int’>	250
PRIMER_SEQUENCING_ACCURACY	<class ‘int’>	20
PRIMER_WT_END_QUAL	<class ‘float’>	0.0
PRIMER_INTERNAL_WT_END_QUAL	<class ‘float’>	0.0
`SEQUENCE_PRIMER_OVERHANG`	<class ‘str’>
`SEQUENCE_PRIMER_REVCOMP_OVERHANG`	<class ‘str’>
`PRIMER_USE_OVERHANGS`	<class ‘bool’>	False
`PRIMER_LONG_OK`	<class ‘bool’>	False
`PRIMER_MIN_ANNEAL_CHECK`	<class ‘int’>	12
`_SEQUENCE_LONG_OVERHANG`	<class ‘str’>
`_SEQUENCE_REVCOMP_LONG_OVERHANG`	<class ‘str’>

Extra/Special Parameters¶

class primer3plus.params.ExtraTypes[source]¶

Extra Parameter types not included in standard Primer3 behavior.

PRIMER_LONG_OK = <ParameterType PRIMER_LONG_OK <class 'bool'> default=False>¶: specifies BoulderIO use long primers (>35bp).

PRIMER_MIN_ANNEAL_CHECK = <ParameterType PRIMER_MIN_ANNEAL_CHECK <class 'int'> default=12>¶: specifies min bases to check for mispriming during primer designs

PRIMER_USE_OVERHANGS = <ParameterType PRIMER_USE_OVERHANGS <class 'bool'> default=False>¶: extra parameter specifies to use primer overhangs in the design

SEQUENCE_PRIMER_OVERHANG = <ParameterType SEQUENCE_PRIMER_OVERHANG <class 'str'> default=>¶: extra parameter specifies the sequence of the left primer overhang

SEQUENCE_PRIMER_REVCOMP_OVERHANG = <ParameterType SEQUENCE_PRIMER_REVCOMP_OVERHANG <class 'str'> default=>¶: extra parameter specifies the sequence of the right primer overhang