teemi.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.
USER_enzyme(amplicon)	Simulates digestion with USER enzyme.
add_feature_annotation_to_seqrecord(sequence)	Adds feature, label and name to a Bio.Seqrecord sequence.
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.
crispr_db_break_location(start_location, …)	Determine the CRISPR cut location in the genome.
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
find_all_occurrences_of_a_sequence(sequence, …)	Searches for all occurrences of a given sequence in a given string.
find_sequence_location(sequence, …)	Finds start and end location of a mathced sequence.
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.
remove_features_with_negative_loc(record)	Removes a SeqFeatures if negative.
seq_to_annotation(seq_record_from, …)	Anotate an Bio.SeqRecord object from another bio.seqrecord object.