teemi.design.combinatorial_design

This part of the design module is used for making combinatorial libraries from DNA fragments.

Functions

assembly_maker(combinatorial_list_of_amplicons)	Assembles Amplicons with pad and makes new overlapping primers.
count_unique_parts(predictions_df, …)	Iterates through the DataFrame of predictions and saves newly encountered parts.
get_assembly_figure(assembly_list[, limit])	Generates a figure for the specified assembly in the assembly list.
get_combinatorial_list(input_list)	Generates all possible combinations from a list of lists.
get_primers(assemblies, names, primer_temps)	Returns a list of ALL primers from the combinatorial library, updates names and what they anneal to.
get_systematic_names(parts_list)	Returns a list of list with systematic names i.e [1,1,1], [1,2,1].
simple_amplicon_maker(list_of_seqs, …[, …])	Creates amplicons, updates their names
unique_amplicons(list_of_assemblies)	Finds Unique amplicons from a list of assemblies :param list_of_assemblies: list of the combinatorial libarary with overlapping ends :type list_of_assemblies: list[[pydna.amplicon.Amplicon]]
unique_primers(primers, list_of_assemblies)	Finds unique primers from a list of assemblies :param primers: a list of all the primers made for the combinatorial library :type primers: list[list[list[pydna.primer.Primer]]] :param list_of_assemblies: used here to update the names of the primers :type list_of_assemblies: list[[pydna.amplicon.Amplicon]]

Classes

DesignAssembly(list_of_seqs, list_of_pads, …)

Make a combinatorial library from DNA fragments.