primerize.primerize_1d Module¶

class primerize.primerize_1d.Primerize_1D(*args, **kwargs)¶

Bases: Singleton

Construct a worker for 1D Primer Design (Simple Assembly).

Parameters:

• MIN_TM – float: (Optional) Minimum annealing temperature for overlapping regions. Unit in Celsius. Positive number only.

• NUM_PRIMERS – int: (Optional) Exact limit of number of primers in design. Non-negative even number only. 0 represents “No limit”.

• MIN_LENGTH – int: (Optional) Minimum length allowed for each primer. Positive number only.

• MAX_LENGTH – int: (Optional) Maximum length allowed for each primer. Positive number only.

• COL_SIZE – int: (Optional) Column width for assembly output. Positive number only.

• WARN_CUTOFF – int: (Optional) Threshold of pairing region length for misprime warning. Positive number only.

• prefix – str: (Optional) Construct prefix/name.

Returns:

primerize.Primerize_1D

Note

This class follows the singleton pattern so that only one instance is created. An instance is already initialized as primerize.Primerize_1D.

__repr__()¶

Representation of the Primerize_1D class.

design(sequence, MIN_TM=None, NUM_PRIMERS=None, MIN_LENGTH=None, MAX_LENGTH=None, prefix=None)¶

Run design code to get a PCR Assembly solution for input sequence under specified conditions. Current worker parameters are used for nonspecified optional arguments.

Parameters:

• sequence – str: Sequence for assembly design. Valid RNA/DNA sequence only, case insensitive.

• MIN_TM – float: (Optional) Minimum annealing temperature for overlapping regions.

• NUM_PRIMERS – int: (Optional) Exact limit of number of primers in design.

• MIN_LENGTH – int: (Optional) Minimum length allowed for each primer.

• MAX_LENGTH – int: (Optional) Maximum length allowed for each primer.

• prefix – str: (Optional) Construct prefix/name.

Returns:

primerize.Design_Single

get(key)¶

Get current worker parameters.

Parameters:

key – str: Keyword of parameter. Valid keywords are 'MIN_TM', 'NUM_PRIMERS', 'MIN_LENGTH', 'MAX_LENGTH', 'prefix'; case insensitive.

Returns:

value of specified key.

Raises:

AttributeError – For illegal key.

reset()¶

Reset current worker parameters to default.

set(key, value)¶

Set current worker parameters.

Parameters:

• key – str: Keyword of parameter. Valid keywords are the same as get().

• value – (auto): New value for specified keyword. Type of value must match key.

Raises:

• AttributeError – For illegal key.

• ValueError – For illegal value.