constrain.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. :param combinatorial_list_of_amplicons: the list of pydna.amplicon.Amplicon that you want generate overlapping primers for. :type combinatorial_list_of_amplicons: list[[pydna.amplicon.Amplicon]] :param overlap: How many basepair overlaps :type overlap: int = 35.
combinatorial_list_maker(...)	Makes all possible combinations from a list of list.
count_unique_parts(df, max_combinations)	Iterate through the list of predictions and save new encountered parts.
empty_list_maker(list_of_sequences)	returns empty list in the length of seqs
get_primers(List_of_assemblies, ...)	Returns a list of ALL primers from the combinatorial library, updates names and what they anneal to.
making_assembled_contigs(...)	Assembles a list of assembly object into linear contigs.
making_assembly_objects(list_of_assemblies)	Assembling amplicons into assembling class that shows fragments, limit,nodes and which algorithm that was used for assembling.
simple_amplicon_maker(list_of_seqs, ...[, ...])	Creates amplicons, updates their names
systematic_names_function(List_of_list_parts)	Returns a list of list with systematic names i.e [1,1,1], [1,2,1].
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[[pydna.primer.Primer, 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_names, ...)

Class able to make a combinatorial library from DNA fragments.