AssemblyTron.Error_prone_PCR_Golden_Gate package

Submodules

AssemblyTron.Error_prone_PCR_Golden_Gate.Error_prone_PCR_writer module

A writer script for generating an Error prone PCR Protocol Script with separate PCRs in OpenTrons API.

This script allows users to perform Error prone PCR where fragments for each assembly are amplified in separate tubes and uses a gradient thermocycler or the 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.Error_prone_PCR_Golden_Gate.GoldenGate_digests_separatepcrruns_gradient_writer module

A writer script for generating a Golden Gate assembly Protocol Script with separate PCRs and digested destination vectors in OpenTrons API.

This script allows users to perform Golden Gate assembly where fragments for each assembly are amplified in separate tubes and backbone fragments are placed on the deck. It uses a gradient thermocycler or the 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.Error_prone_PCR_Golden_Gate.GoldenGate_separatepcrruns_gradient_writer module

A writer script for generating a Golden Gate assembly Protocol Script with separate PCRs and NO digested destination vectors in OpenTrons API.

This script allows users to perform Golden Gate assembly where fragments for each assembly are amplified in separate tubes. It uses a gradient thermocycler or the 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.Error_prone_PCR_Golden_Gate.Setup_Error_prone_PCR module

Setup script for Error prone PCR. This variation of the writer is for when no entry plasmids are being used.

This script walks the user through setup of Error prone PCR. 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 to be installed in the python environment where running.

This script can also be called as a module by calling AssemblyTron.Error_prone_PCR_Golden_Gate.Setup_Error_prone_PCR.

AssemblyTron.Error_prone_PCR_Golden_Gate.Setup_Error_prone_PCR_NOdigest module

Setup script for Error prone PCR. This variation of the writer is for when no entry plasmids are being used.

This script walks the user through setup of Error prone PCR. 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.Error_prone_PCR_Golden_Gate.Setup_Error_prone_PCR_NOdigest.

AssemblyTron.Error_prone_PCR_Golden_Gate.Setup_STD_GoldenGate_Assembly module

Setup script for stage 3 Golden Gate Assembly with with NO destination plasmid.

This script walks the user through setup of a 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.Error_prone_PCR_Golden_Gate.Setup_STD_GoldenGate_Assembly.

AssemblyTron.Error_prone_PCR_Golden_Gate.Setup_STD_GoldenGate_digests_Assembly module

Setup script for stage 3 Golden Gate Assembly with with a destination plasmid with restriction sites

This script walks the user through setup of a Golden Gate assembly with a destination plasmid with restriction sites. 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.Error_prone_PCR_Golden_Gate.Setup_STD_GoldenGate_digests_Assembly.

AssemblyTron.Error_prone_PCR_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

This script contains a protocol for diluting up to 24 primers and templates to concentrations specified in the AssemblyTron.Error_prone_pcr.1_Setup_STD_GoldenGate_digests_PCR 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.Error_prone_PCR_Golden_Gate.dilution_Error_prone_PCR_writer module

A writer script that creates a Dilution Script in OpenTrons API for the error prone PCR fragments in stage 2.

This script contains a protocol for diluting primers and templates to concentrations specified in the AssemblyTron.Error_prone_pcr.Setup_Error_prone_PCR 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: