AssemblyTron.Cloning package¶
Submodules¶
AssemblyTron.Cloning.IVA_separatepcrruns_gradient_writer module¶
A writer script for generating a Homology Dependent Assembly Protocol Script with separate PCRs in OpenTrons API.
This script allows users to perform Homology dependent assembly where fragments for each assembly are amplified in separate tubes and uses a gradient thermocycler. This protocol is thoroughly validated and robust, so we recommend using it.
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.Cloning.Setup_seppcr_gradient_24 module¶
Setup script for Homology Dependent Assembly with 24 tube capacity
This script walks the user through setup of a homology dependent assembly with up to 24 combined primers and templates. 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.Cloning.Setup_seppcr_gradient_24.
AssemblyTron.Cloning.Setup_seppcr_gradient_96 module¶
Setup script for Homology Dependent Assembly with 96 tube capacity
This script walks the user through setup of a homology dependent assembly with up to 96 combined primers and templates. 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.Cloning.Setup_seppcr_gradient_96.
AssemblyTron.Cloning.dilution_24_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.Cloning.Setup_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.Cloning.dilution_96_writer module¶
A writer script that creates a Dilution Script in OpenTrons API for up to 96 primers and templates
This script contains a protocol for diluting up to 96 primers and templates to concentrations specified in the AssemblyTron.Cloning.Setup_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.