set_seq_vh_vbΒΆ

You can download the script here.

Used for changing sequences in an origami, particularly making sticky ends, and prints out the new topology file.

Usage:

python set_seq_vh_vb.py conf_file top_file virt2nuc seq_file
Args:
  • conf_file: configuration file
  • top_file: topology file
  • virt2nuc: virt2nuc file (can be generated from cadnano_interface.py with a cadnano json file)
  • seq_file: file containing which base to change (details described below)
Notes:

An example seq_file is shown below:

0 16-23 stap ATCGATCG

This will change the sequence for the specified (vh, vb, type) to ATCGATCG. vh and vb stands for virtual base index and virtual helix index in cadnano, and type is either stap (staple) or scaf (scaffold).