constrain.design.cloning

Module used for cloning of microbial strains.

Functions

CAS9_cutting(gRNA_record, background_record)	Simulates double-stranded-break by CAS9 given a gRNA.
CRIPSR_knockout(gRNA_record, insertion_site, ...)	Simple version of casembler - Cuts the insertion site with
UPandDW(strain, isite_name[, path_to_gRNA_table])	Finds upstream and downstream sequences based on genome and site name.
USER_enzyme(amplicon)	Simulates digestion with USER enzyme.
casembler(bg_strain[, site_names, gRNAs, ...])	Simulate in vivo assembly and integration with the possibility of printing to gb files or send it directly to benchling.
extract_gRNAs(template, name)	Extracts gRNAs from a template.
extract_sites(annotations, templates, names)	This function extracts the sequences from annotated sequences based on their names
extract_template_amplification_sites(...)	Extracts amplifications sites from a templates features
multiply_list(myList)	Multiplies elements one by one.
nicking_enzyme(vector)	Nt.Bbc.CI (nicking enzyme, Nicks) a vector with the sequence 'CGCGTG' on watson and 'CGCACG' on crick strand.
plate_plot(df, value)	Plots a 96 well plate as a pandas df.
recs_no_duplicates(recs_with_duplicates)	Removes duplicate sequences from a list.
recs_no_duplicates_names(recs_with_duplicates)	Removes duplicate names from a list
remove_features_with_negative_loc(record)	Removes a SeqFeatures if negative.
remove_tuple_duplicates(lst)	Removes tuple duplicates
seq_to_annotation(seqrec_from, seqrec_onto, ...)	Anotate an amplicon object from another amplicon object.