primerize.util Module¶

primerize.util.DNA2RNA(sequence)¶

Convert a DNA sequence input to RNA.

Parameters:	sequence -- str: Input DNA sequence.
Returns:	str -- String of RNA

primerize.util.RNA2DNA(sequence)¶

Convert a RNA sequence input to DNA.

Parameters:	sequence -- str: Input RNA sequence.
Returns:	str -- String of DNA

primerize.util.complement(sequence)¶

Convert a DNA sequence input to its complement strand.

Parameters:	sequence -- str: Input DNA sequence.
Returns:	str -- String of complement DNA strand.
Raises:	ValueError -- For illegal sequence.

primerize.util.coord_to_num(coord)¶

Convert a 96-Well Coordinate string to number (1-based).

Parameters:	coord -- str: Input WellPosition coordinate string, e.g. 'A01'.
Returns:	int or None if illegal input.

primerize.util.diff_bps(structures, offset=0, flag=True)¶

Find base-pairs that are not present in all secondary structure inputs. Each input secondary structure is compared to all the others.

Parameters:	structures -- list(str): Input secondary structures. offst -- int: (Optional) Index numbering offset for output numbers. flag -- bool: (Optional) Overriding flag for excluding shared helices.
Returns:	list(list(tuple(int, int))) -- List of helices, and each helix is a list of tuple of base-pairs with their seqpos.

primerize.util.get_mut_range(mut_start, mut_end, offset, sequence)¶

Validate and calculate mutation range based on input sequence and offset. If mutation range exceeds possible range, the maximum possible range is returned.

Parameters:	mut_start -- int: Lower limit of mutation range, should be based on offset. mut_end -- int: Upper limit of mutation range, should be based on offset. offset -- int: Index numbering offset. sequence -- str: The sequence (length used).
Returns:	(which_muts, mut_start, mut_end) which_muts - list(int): The final range of mutations. mut_start - int: The valid mut_start. mut_end - int: The valid mut_end.

primerize.util.get_mutation(nt, lib)¶

Mutate a single nucleotide.

Parameters:	nt -- str: The nucleotide of interest. lib -- int: The mutation library choice; choose from (1, 2, 3, 4): * 1 represents "A->U, U->A, C->G, G->C", * 2 represents "A->C, U->C, C->A, G->A", * 3 represents "A->G, U->G, C->U, G->U", * 4 represents "A->C, U->G, C->A, G->U", * 5 represents "A->C, U->G, C->G, G->C".
Returns:	str
Raises:	ValueError -- For illegal lib input.

primerize.util.num_to_coord(num)¶

Convert a 96-Well Coordinate number (1-based) to string.

Parameters:	num -- int: Input WellPosition coordinate number, e.g. 96.
Returns:	str or None if illegal input.

primerize.util.reverse(sequence)¶

Convert a DNA sequence input to its reverse order.

Parameters:	sequence -- str: Input DNA sequence.
Returns:	str -- String of reverse DNA strand.

primerize.util.reverse_complement(sequence)¶

Convert a DNA sequence input to its reverse complement strand.

Parameters:	sequence -- str: Input DNA sequence.
Returns:	str -- String of reverse complement DNA strand.

primerize.util.str_to_bps(structure, offset=0)¶

Convert a dot-bracket secondary structure into base-pair tuples.

Parameters:	structure -- str: Input secondary struture. offset -- int: (Optional) Index numbering offset for output numbers.
Returns:	list(list(tuple(int, int))) -- List of helices, and each helix is a list of tuple of base-pairs with their seqpos.

primerize.util.valid_WC_pair(nt_1, nt_2)¶

Check if two nucleotides form a valid Watson-Crick base-pair.

Parameters:	nt_1 -- str: Nucleotide. nt_2 -- str: Nucleotide.
Returns:	bool