AssemblyTron.Golden_Gate package

Submodules

AssemblyTron.Golden_Gate.GoldenGate_digests_separatepcrruns_gradient_writer module

A writer script for generating a Golden Gate Assembly Protocol Script with separate PCRs and digested entry plasmids in OpenTrons API.

This script allows users to perform Golden Gate assembly where fragments for each assembly are amplified in separate tubes and uses a gradient thermocycler or on deck thermocycler.

This script generates a text file that runs on the OT-2 via the run app. It calls CSVs to make a customized protocol script. This script is designed to run on a personal computer on the command line.

AssemblyTron.Golden_Gate.GoldenGate_nodigests_separatepcrruns_gradient_writer module

A writer script for generating a Golden Gate Assembly Protocol Script with separate PCRs and NO digested entry plasmids in OpenTrons API.

This script allows users to perform Golden Gate assembly where fragments for each assembly are amplified in separate tubes and uses a gradient thermocycler or on deck thermocycler.

This script generates a text file that runs on the OT-2 via the run app. It calls CSVs to make a customized protocol script. This script is designed to run on a personal computer on the command line.

AssemblyTron.Golden_Gate.Setup_digests_gradient module

Setup script for Golden Gate Assembly. This variation of the writer is for when entry plasmids are being used.

This script walks the user through setup of Golden Gate assembly. This script makes a dated directory in the wd, parses/transfers input files, allows users to customize parameters, runs the gradient PCR optimization algorithm, and performs calculation and tracking steps for parsed design files.

This script requires no arguments, but instead obtains all necessary information and files by user-friendly tkinter pop-up windows.

This script requires pandas , numpy , shutil , tkinter to be installed in the python environment where running.

This script can also be called as a module by calling AssemblyTron.Golden_Gate.Setup_digests_gradient.

AssemblyTron.Golden_Gate.Setup_nodigests_seppcr_gradient_24 module

Setup script for Golden Gate Assembly. This variation of the writer is for when NO entry plasmids are being used and has a 24 tube capacity.

This script walks the user through setup of Golden Gate assembly. This script makes a dated directory in the wd, parses/transfers input files, allows users to customize parameters, runs the gradient PCR optimization algorithm, and performs calculation and tracking steps for parsed design files.

This script requires no arguments, but instead obtains all necessary information and files by user-friendly tkinter pop-up windows.

This script requires pandas , numpy , shutil , tkinter to be installed in the python environment where running.

This script can also be called as a module by calling AssemblyTron.Golden_Gate.Setup_nodigests_seppcr_gradient_24.

AssemblyTron.Golden_Gate.Setup_nodigests_seppcr_gradient_96 module

Setup script for Golden Gate Assembly. This variation of the writer is for when NO entry plasmids are being used and has a 96 tube capacity.

This script walks the user through setup of Golden Gate assembly. This script makes a dated directory in the wd, parses/transfers input files, allows users to customize parameters, runs the gradient PCR optimization algorithm, and performs calculation and tracking steps for parsed design files.

This script requires no arguments, but instead obtains all necessary information and files by user-friendly tkinter pop-up windows.

This script requires pandas , numpy , shutil , tkinter to be installed in the python environment where running.

This script can also be called as a module by calling AssemblyTron.Golden_Gate.Setup_nodigests_seppcr_gradient_96.

AssemblyTron.Golden_Gate.dilution_24_digests_writer module

A writer script that creates a Dilution Script in OpenTrons API for up to 24 primers and templates for the digested entry plasmid Golden Gate

This script contains a protocol for diluting up to 24 primers and templates to concentrations specified in the AssemblyTron.Golden_Gate.Setup_digests_gradient module.

This script generates a text file that runs on the OT-2 via the run app. It calls CSVs to make a customized protocol script. This script is designed to run on a personal computer on the command line.

AssemblyTron.Golden_Gate.dilution_24_writer module

A writer script that creates a Dilution Script in OpenTrons API for up to 24 primers and templates when there are no digested entry plasmids included in the design.

This script contains a protocol for diluting up to 24 primers and templates to concentrations specified in the AssemblyTron.Golden_Gate.Setup_nodigests_seppcr_gradient_24 module.

This script generates a text file that runs on the OT-2 via the run app. It calls CSVs to make a customized protocol script. This script is designed to run on a personal computer on the command line.

AssemblyTron.Golden_Gate.dilution_96_writer module

A writer script that creates a Dilution Script in OpenTrons API for up to 96 primers and templates when there are no digested entry plasmids included in the design.

This script contains a protocol for diluting up to 96 primers and templates to concentrations specified in the AssemblyTron.Golden_Gate.Setup_nodigests_seppcr_gradient_96 module.

This script generates a text file that runs on the OT-2 via the run app. It calls CSVs to make a customized protocol script. This script is designed to run on a personal computer on the command line.

Module contents

Setup_nodigests_seppcr_gradient_24

This script walks the user through processing assembly design files and making a directory for perfoming Golden Gate Assembly with AssemblyTron.

This script requires the user to have an assembly design built with j5. The main combinatorial design file required is a CSV.

This script require pandas, numpy, to be installed in the python environment in which you are running this script.

This file can also be imported as a module and cotains the following function: