jvrana / dasi-dna-design Goto Github PK

Describe the bug
DASi can design PCR products that are not amplifiable. For example, pcr reactions that have multiple binding sites.

Expected behavior
DASi should detect bad PCRs and heavily penalize their use during the optimization process.

TODO

• make test that forces a bad PCR product.

There are a lot of design parameters, these should be exposed to the user.

test_fake_design

Milestones

1. Implement DNA complexity to efficiency for graphs
2. Implement partitioning for B->A gaps
3. Implement partitioning algorithm to find optimal synthesis partitioning

When designing multiple sequences, DASi should try to optimize the sharing of synthesized fragments to minimize cost

Some sequences are prone to recombination. DASi should detect this and issue a warning.

• minimum bases to find primer using primer3

DASi should be able to produce nice PDF assembly reports for users.

The following modules occasionally fail randomly

• Networkx Utils
• DNA complexity calculations
• Randomized designs

DASi should produce a clear, easy to understand JSON output for its designs.

If num fragments > 4/5 or fragment size > 8Kb, the assembly junction parameters should change (35-40bp overhangs are recommended).

• Creating designs that have sequence similarity
• Creating designs that use pre-prepared DNA fragments
• Creating designs that utilize pre-made primers

The efficiency of a gapped region should be lower for highly complex DNA. Highly complex DNA would be the following:

• less than 25% GC content
• higher than 75% GC content
• homopolymeric runs of 10 or more A/Ts
• homopolymeric runs of 6 or more G/Cs
• repeats greater than 14bp
• hairpins

Describe the bug
The following warning often occurs in the normal execution of DASi
RuntimeWarning: invalid value encountered in true_divide

To Reproduce
Run DASi on any sequence design

Expected behavior
No warnings

Additional context
This occurs in the networkx utilities algorithms.

In many cases, a better assembly may be found with slightly different DNA sequence that results in the same coding sequence:

• In designs, identify CDS
• use tblastn to find fragments that align to goal

• Log to file
• Better logging levels
• Logging for CLI only

Primer annotations in particular are not be carried to the final JSON output.

Describe the bug

Designs occasionally produce this bug:

dasi.exceptions.DasiSequenceDesignException: Sequence is cyclic but there are no precessors for AssemblyNode(index=0, expandable=True, type='A', overhang=False)

Unclear how to reproduce.

When designing multiple sequences, DASi should be able to share PCR products and primers designs in other designs.

Is your feature request related to a problem? Please describe.
There should be default vendor configurations for costs.

Describe the solution you'd like
Vendor considerations
IDT

• Well defined length > cost and time estimates

TWIST

• Produces adapter on each fragment. Primers must be ordered for assemblies in most cases. This optimization procedure is not implemented. For TWIST synthesized fragments, the cost would be equivalent to the synthesis cost + the cost of new primers. There may be optimizations to be had with ordering the TWIST fragment and ordering different primers to amplify the fragment.

consider Design merging methods so each design can run in parallel if desired.

• Better Usage page and Installation page up front
• Better format for JSON Schema
• Point users to use output JSON format

DASi should output a SBOL file as well.

This would be a good starting point: https://pysbol2.readthedocs.io/en/latest/dbtl.html

In many cases, users may not care about the exact sequence between parts (scar sequences) or some degenerate sequence between fusion proteins (GSG linker)