primerize.primerize_3d Module¶

class primerize.primerize_3d.Primerize_3D(*args, **kwargs)¶

Bases: Singleton

Construct a worker for 3D Primer Design (Mutation/Rescue Plates).

Parameters:

• offset – int: (Optional) Sequence numbering offset, which is one minus the final number of the first nucleotide.

• N_mutations – int: (Optional) Number of consecutive mutations for “single mutants”. Valid choices are (1, 2, 3) (e.g. 2 makes “single mutants” like ['G13C', 'T14A'] and “double mutants” like ['G13C', 'T14A', 'A71T', 'C72G']).

• which_lib –

  int: (Optional) Mutation library choice. Valid choices are (1, 4):

  * 1 represents "A:U->U:A, G:C->C:G" library ("swap");
  * 4 represents "A:U->C:G, G:C->U:A" library ("cross");
  * 5 represents "A:U->C:G, G:C->C:G" library ("stable");
  
  Note: G:U pairs are always replaced by C:G pairs.
  

• is_exclude – bool: (Optional) Flag for whether exclude shared helices across structures.

• is_single – bool: (Optional) Flag for whether include single mutants on the plate.

• is_fillWT – bool: (Optional) Flag for whether include Wild-type primers at all WellPositions.

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

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

Returns:

primerize.Primerize_3D

Note

This class follows the singleton pattern so that only one instance is created. An instance is already initialized as primerize.Primerize_3D.

design(sequence, primer_set=[], structures=[], offset=None, N_mutations=None, which_lib=None, which_muts=[], prefix=None, is_exclude=None, is_single=None, is_fillWT=None, is_force=False)¶

Run design code to get library plates for input sequence and structures 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.

• structures – list(str): Array of secondary structures. Use dot-bracket notation. Each structure should be the same length as sequence.

• offset – int: (Optional) Sequence numbering offset.

• N_mutations – int: (Optional) Number of consecutive mutations for “single mutants”.

• which_lib – int: (Optional) Mutation library choice.

• which_muts – list(int): (Optional) Array of mutation positions. Use numbering based on offset. When nonspecified, the entire sequence is included for mutagenesis.

• is_exclude – bool: (Optional) Flag for whether exclude shared helices across structures.

• is_single – bool: (Optional) Flag for whether include single mutants on the plate.

• is_fillWT – bool: (Optional) Flag for whether include Wild-type primers at all WellPositions.

Returns:

primerize.Design_Plate

get(key)¶

Get current worker parameters.

Parameters:

key – str: Keyword of parameter. Valid keywords are 'offset', 'N_mutations', 'which_lib', 'is_exclude', 'is_single', 'is_fillWT', '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.