primerize.primerize_2d Module¶

class primerize.primerize_2d.Primerize_2D(*args, **kwargs)¶

Bases: 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.