AssemblyTron package

Subpackages

• AssemblyTron.Cloning package
  • Submodules
  • AssemblyTron.Cloning.IVA_separatepcrruns_gradient_writer module
  • AssemblyTron.Cloning.Setup_seppcr_gradient_24 module
  • AssemblyTron.Cloning.Setup_seppcr_gradient_96 module
  • AssemblyTron.Cloning.dilution_24_writer module
  • AssemblyTron.Cloning.dilution_96_writer module
  • Module contents
• AssemblyTron.Error_prone_PCR_Golden_Gate package
  • Submodules
  • AssemblyTron.Error_prone_PCR_Golden_Gate.Error_prone_PCR_writer module
  • AssemblyTron.Error_prone_PCR_Golden_Gate.GoldenGate_digests_separatepcrruns_gradient_writer module
  • AssemblyTron.Error_prone_PCR_Golden_Gate.GoldenGate_separatepcrruns_gradient_writer module
  • AssemblyTron.Error_prone_PCR_Golden_Gate.Setup_Error_prone_PCR module
  • AssemblyTron.Error_prone_PCR_Golden_Gate.Setup_Error_prone_PCR_NOdigest module
  • AssemblyTron.Error_prone_PCR_Golden_Gate.Setup_STD_GoldenGate_Assembly module
  • AssemblyTron.Error_prone_PCR_Golden_Gate.Setup_STD_GoldenGate_digests_Assembly module
  • AssemblyTron.Error_prone_PCR_Golden_Gate.dilution_24_digests_writer module
  • AssemblyTron.Error_prone_PCR_Golden_Gate.dilution_Error_prone_PCR_writer module
  • Module contents
    • Setup_nodigests_seppcr_gradient_24
• AssemblyTron.Golden_Gate package
  • Submodules
  • AssemblyTron.Golden_Gate.GoldenGate_digests_separatepcrruns_gradient_writer module
  • AssemblyTron.Golden_Gate.GoldenGate_nodigests_separatepcrruns_gradient_writer module
  • AssemblyTron.Golden_Gate.Setup_digests_gradient module
  • AssemblyTron.Golden_Gate.Setup_nodigests_seppcr_gradient_24 module
  • AssemblyTron.Golden_Gate.Setup_nodigests_seppcr_gradient_96 module
  • AssemblyTron.Golden_Gate.dilution_24_digests_writer module
  • AssemblyTron.Golden_Gate.dilution_24_writer module
  • AssemblyTron.Golden_Gate.dilution_96_writer module
  • Module contents
    • Setup_nodigests_seppcr_gradient_24
• AssemblyTron.MoClo_builder package
  • Submodules
  • AssemblyTron.MoClo_builder.MoClo_writer module
  • AssemblyTron.MoClo_builder.Setup_MoClo module
  • Module contents

Submodules

AssemblyTron.Update_Input module

Input.csv Updater

This updater script is to ensure the robot calls the correct Input.csv file. Failure to complete this step could result in errors and failure.

This script requires pandas to be installed in the python environment where running.

This script is run as a module on the command line with the command AssemblyTron.Update_Input.py or if it is being run from a subdirectory the command would be AssemblyTron.{subdirectory folder}.{dated folder}.1_Update_Input.py

AssemblyTron.j5_to_csvs module

AssemblyTron j5 parsing script

This script guides the user through finding the j5 DNA assembly design saved on their local machine.

The script does not require any input files, and it transfers parsed CSV files to the correct directory in AssemblyTron.

This script requires that pandas be installed in the python environment where the script is run.

This script should not be executed except when copied to a folder with a j5 combinatorial design file, and then it can also be run as a module by calling AssemblyTron.j5_to_csvs

AssemblyTron.j5_to_csvs_digests module

AssemblyTron j5 parsing script. This variation of the script accomodates desingns that inculde destination plasmid backbones. It functions similarly to j5_to_csvs

This script guides the user through finding the j5 DNA assembly design saved on their local machine.

The script does not require any input files, and it transfers parsed CSV files to the correct directory in AssemblyTron.

This script requires that pandas be installed in the python environment where the script is run.

This script should not be executed except when copied to a folder with a j5 combinatorial design file, and then it can also be run as a module by calling AssemblyTron.j5_to_csvs_digests

AssemblyTron.opentrons_demo_script module

OT-2 Demo Script

This is a demo script designed to be executed on the OT-2 run app. It shows the OT-2 in action.

This script does not require any input files.

AssemblyTron.pathswriter module

AssemblyTron Paths Writer Script

This script guides the user through finding and recording the AssemblyTron working directory and the Rscript.exe file. The pathswriter module records working directory and enables protocol setup scripts to navigate accurately. The pathswriter.py must be run in the AssemblyLine working directory so that the correct path is generated, and the paths.csv file is saved in the proper location.

The script does not require any input files, however it saves the paths as strings in a CSV.

This script requires that pandas be installed in the python environment where the script is run.

This file can also be run as a module by calling AssemblyTron.pathswriter

AssemblyTron.static_wired_IP_address module

Static wired IP address script

This script was provided by Opentrons and is used to set a Static IP address for your OT-2. The static IP address is crucial for automating transfer of CSV files between the AssemblyTron working directory and the OT-2.

This script requires the new static IP address, which should be selected by your IT administrator.

Module contents