Sequence Database
- save filename and path for SeqRecord on load
better way to add notes to graph edge
graph post-processing config
Remov 'cost' key from edge data (it is not used)
- Make a new class called DesignConfig
- Should contain min_primer_anneal. This value should be used for calculating primer3 design parameters (as in primer3plus.utils.anneal). This same value minus one, should be used to find misprimings in the Graph post processor. User should be able to relax or tighten the post processor.
- Could contain n_jobs, n_paths
- Other post processor parameters
- cost parameters?
- shared templates? select from same templates, if possible
- shared sequences and fragments?
- shared primers?
- Implement ability to partition B->A edges. DONE.
- Implement complexity to efficiency score for all gapped plasmids
Other
- Resolve TODOs
- Basic design of sequences
- avoiding homology repeats
- sharing primer designs across multiple designs
- sharing fragments across multiple designs
- add a level inbetween INFO and ERROR for logger for status update to CLI
- add log to text file
Gap partitioning
Partition Score: https://colab.research.google.com/drive/19YZ7Jnx-4cfJAbNoDF7wgMheCqRCehPZ
**