primerize.primerize_1d Module¶

class primerize.primerize_1d.Primerize_1D(MIN_TM=60.0, NUM_PRIMERS=0, MIN_LENGTH=15, MAX_LENGTH=60, COL_SIZE=142, WARN_CUTOFF=3, prefix='primer')¶

Bases: primerize.thermo.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.