primerize.primerize_3d Module¶

class primerize.primerize_3d.Primerize_3D(offset=0, N_mutations=1, which_lib=1, is_exclude=False, is_single=True, is_fillWT=False, COL_SIZE=142, prefix='lib')¶

Bases: primerize.thermo.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.