teemi.build.PCR

This part of the lab module is used for simulating and calculating PCR reactions.

Functions

Q5_NEB_PCR_program(amplicon)	Simple PCR program designed to give a quick visual representation of a PCR reaction.
amplicon_by_name(name, amplicons_lst)	Returns amplicon with specified name.
calculate_elongation_time(amplicon)	Determines elongation time for an amplicon and add the elongation time to the amplicon annotations.
calculate_processing_speed(amplicon)	Determines process speed based on the which polymerase is used.
calculate_required_thermal_cyclers(…[, …])	Determines the number of thermalcyclers that is needed based on elongation time differences
calculate_volumes([vol_p_reac, …])	Makes a reaction scheme for PCR master mixes.
get_amplicons_by_column(col, amplicon_df, …)	Returns a list of amplicons in a given gel column.
get_amplicons_by_row(row, amplicon_df, amplicons)	Returns a list of amplicons in a given gel row.
grouper(iterable, max_diff)	Groups objects into distinct groups based on differences
nanophotometer_concentrations([path])	Reads a CSV file with nanophotometer concentraions and returns the concentrations in a list.
pcr_locations(amplicons)	Obtain annotation information for amplicons.
primer_ta_neb(primer1, primer2[, conc, prodcode])	Calculates primer pair melting temp TA, from NEB.
primer_tm_neb(primer[, conc, prodcode])	Calculates a single primers melting temp from NEB.
set_plate_locations(amplicons)	Makes a dataframe from amplicons.
update_amplicon_annotations(amplicon_names, …)	Updates the annotations of amplicons in the amplicon list.