primerize.primerize_2d Module¶

class primerize.primerize_2d.Primerize_2D(offset=0, which_muts=[], which_lib=1, COL_SIZE=142, prefix='lib')¶

Bases: primerize.thermo.Singleton

Construct a worker for 2D Primer Design (Mutate-and-Map Plates).

Parameters:

offset -- int: (Optional) Sequence numbering offset, which is one minus the final number of the first nucleotide. which_muts -- list(int): (Optional) Array of mutation positions. Use numbering based on offset. When nonspecified, the entire sequence is included for mutagenesis. which_lib -- int: (Optional) Mutation library choice. Valid choices are (1, 2, 3): * 1 represents "A->U, U->A, C->G, G->C" library; * 2 represents "A->C, U->C, C->A, G->A" library; * 3 represents "A->G, U->G, C->U, G->U" library. COL_SIZE -- int: (Optional) Column width for assembly output. Positive number only. prefix -- str: (Optional) Construct prefix/name.

Returns:

primerize.Primerize_2D

Note

This class follows the singleton pattern so that only one instance is created. An instance is already initialized as primerize.Primerize_2D.

design(sequence, primer_set=[], offset=None, which_muts=None, which_lib=None, prefix=None, is_force=False)¶

Run design code to get library plates for input sequence according to specified library options. Current worker parameters are used for nonspecified optional arguments.

Parameters:	job_1d -- primerize.Design_Single: Result of primerize.Primerize_1D.design(). Its sequence, primer_set, and prefix are used. offset -- int: (Optional) Sequence numbering offset. which_muts -- list(int): (Optional) Array of mutation positions. which_lib -- int: (Optional) Mutation library choice.
Returns:	primerize.Design_Plate

get(key)¶

Get current worker parameters.

Parameters:	key -- str: Keyword of parameter. Valid keywords are 'offset', 'which_muts', 'which_lib', 'COL_SIZE', '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.