primerize.util_class Module¶

class primerize.util_class.Assembly(sequence, primers, name, COL_SIZE=142)¶

Bases: object

Collection of result data essential for drawing an assembly scheme.

Parameters:

• sequence – str: Sequence of assembly design.

• primers – list(list(int): Numeric representation (end numbering and direction) of primers.

• name – str: Construct prefix/name.

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

sequence¶

str: Sequence of assembly design.

primers¶

list(list(int)): Numeric representation (end numbering and direction) of primers.

name¶

str: Construct prefix/name.

bp_lines¶

list(str): Strings for base-pairing lines ('|').

seq_lines¶

list(str): Strings for primer sequence lines.

print_lines¶

list(tuple(str, str)): Strings for all lines assembled, i.e. list(tuple('marker', 'print_line')).

Tm_overlaps¶

list(float): List of melting temperature for all overlapping regions.

__repr__()¶

Representation of the Assembly class.

__str__()¶

Results of the Assembly class. Calls echo().

echo()¶

Print result in rich-text.

Returns:

str

save(path='./', name=None)¶

Save result to text file.

Parameters:

• path – str: (Optional) Path for file saving. Use either relative or absolute path.

• name – str: (Optional) Prefix/name for file name. When nonspecified, current object’s name is used.

class primerize.util_class.Construct_List¶

Bases: object

Collection of mutant constructs. An empty isntance of primerize.Mutation is always initiated as the first element, i.e. a Wild-type well as the first of list.

_data¶

Data of constructs, in format of list(primerize.Mutation).

__contains__(mut_list)¶

Test if a list of given mutant construct is present.

Parameters:

mut_list – primerize.Mutation: A mutant represented by primerize.Mutation.

Returns:

bool

__iter__()¶

Iterator through all constructs.

__len__()¶

Number of filled wells.

Returns:

int

__repr__()¶

Representation of the Construct_List class.

__str__()¶

Results of the Construct_List class. Calls echo().

echo(prefix='')¶

Print result in rich-text.

Returns:

str

list()¶

Return a list of all constructs.

Returns:

list(list(str))

merge(other)¶

Merge 2 lists of constructs.

Parameters:

other – primerize.Construct_List: Another list of constructs.

Returns:

primerize.Construct_List – A list of duplicated constructs between inputs.

Raises:

TypeError – For illegal other.

pop(mut_list)¶

Remove a list of mutations.

Parameters:

mut_list – primerize.Mutation: A mutant represented by primerize.Mutation. Mutant that is not present will result in a premature return with False.

Returns:

bool – Whether mut_list is successfully removed.

push(mut_list)¶

Add a list of mutations.

Parameters:

mut_list – primerize.Mutation: Mutations. A mutant represented by primerize.Mutation. If the mutant is already present, it will return False.

Returns:

bool – Whether mut_list is successfully added.

class primerize.util_class.Mutation(mut_str=[])¶

Bases: object

Collection of mutations for a construct.

Parameters:

mut_list – list(str): (Optional) List of mutations. When nonspecified, an empty instance is created; when specified, it calls push(). An empty instance means no mutations, i.e. Wild-type.

_data¶

Data of mutations, in format of dict: { int: tuple(str, str) }, i.e. dict: {'seqpos': ('wt_char', 'mut_char') }.

__contains__(mut_str)¶

Test if a list of given mutation is present.

Parameters:

mut_list – list(str): Mutations in format of 'wt_char', 'seq_pos', 'mut_char', (e.g. ['G13C', 'A15T']).

Returns:

bool

__eq__(other)¶

Comparison method for whether two Mutation objects contain the same set of mutations.

__iter__()¶

Iterator through all mutations.

__len__()¶

Number of filled wells.

Returns:

int

__repr__()¶

Representation of the Mutation class.

__str__()¶

Results of the Mutation class. Calls echo().

echo()¶

Print result in rich-text, delimited by ';'.

Returns:

str

list()¶

Return a list of all mutations.

Returns:

list(str)

merge(other)¶

Merge 2 lists of mutations.

Parameters:

other – primerize.Mutation: Another list of mutations.

Raises:

TypeError – For illegal other.

pop(mut_str)¶

Remove a list of mutations.

Parameters:

mut_list – list(str): Mutations. Valid keywords are the same as has(). Mutations that are not present will result in a premature return with False.

Returns:

bool – Whether all mutations in mut_list are successfully removed.

push(mut_str)¶

Add a list of mutations.

Parameters:

mut_list – list(str): Mutations. Valid keywords are the same as has(). Each 'seq_pos' can only be mutated once. Conflicting mutations are overwritten and the most recent one is saved. 'WT' is ignored.

Raises:

ValueError – For illegal mut_str.

class primerize.util_class.Plate_96Well(tag=1)¶

Bases: object

Abstraction of 96-well plates.

Parameters:

tag – int: (Optional) Mutation library tag. Use which_lib number.

coords¶

set(str): Filled 96-Well Coordinates.

_data¶

Data of primers and names, in format of dict: { str: tuple(primerize.Mutation, str) }, i.e. dict: {'coord': ('tag', 'primer') }.

__contains__(coord)¶

Test if data of a given WellPosition is present.

Parameters:

coord – str: WellPosition (e.g. 'A01') for data.

Returns:

bool

__len__()¶

Number of filled wells.

Returns:

int

__repr__()¶

Representation of the Plate_96Well class.

__str__()¶

Results of the Plate_96Well class. Calls echo().

echo(ref_primer='')¶

Print result in rich-text.

Parameters:

ref_primer – list(str): (Optional) List of Wild-type primer_set for highlighting. If nonspecified, highlighting is disabled.

Returns:

str

get(coord)¶

Get data of a particular well or number of wells filled.

Parameters:

coord – str: Keyword of parameter. Use WellPosition for well data.

Returns:

value of specified coord.

Raises:

• AttributeError – For illegal WellPosition (out of range(0, 96) + 1).

• KeyError – For nonexisted coord.

reset()¶

Clear current plate data.

save(ref_primer='', file_name='./plate.svg', title='')¶

Save plate layout to image file (SVG).

Parameters:

• ref_primer – list(str): (Optional) List of Wild-type primer_set for highlighting. If nonspecified, highlighting is disabled.

• file_name – str: (Optional) File name. Include path into file_name when specifying. Use either relative or absolute path.

• title – str: (Optional) Title to display on image. LaTex NOT supported.

set(coord, tag, primer)¶

Record data of a particular well.

Parameters:

• coord – str: WellPosition for data. Use same range as get(). Existing data for the same well is overwritten.

• tag – primerize.Mutation: Mutant representd by primerize.Mutation. str is only supported for backward compatibility.

• primer – str: Primer seuqence of well. Use sense-strand.

Raises:

AttributeError – For illegal WellPosition.