[Feature]: Add support for circular sequences #5
Description
Feature Type
New algorithm or analysis method
Problem Description
One of the most useful features missing from Prodigal is support for gene calling on circular sequences. Providing this capability in Orphos would be highly valuable.
Previous discussions about this feature can be found at:
- Support for circular sequences althonos/pyrodigal#67
- support detection of RBS across linear chromosome breakpoint ? althonos/pyrodigal#65
Proposed Solution
I'd like Orphos to enable gene calling that explicitly accounts for the circular structure of sequences. In this mode, the last and first bases of a sequence would be treated as adjacent, allowing genes to span the sequence breakpoint.
Use Case
This feature is useful when processing genomes with circular topology, such as bacterial chromosomes, plasmids, and some viruses. It is especially useful for metagenomic data, where rotating all sequences to a standard start point is impractical.
Alternatives Considered
No response
Examples
Priority
Low (nice to have)
Implementation Ideas
No response
Additional Context
No response
Checklist
- I have searched existing issues to ensure this feature hasn't been requested before
- I have checked the documentation to ensure this feature doesn't already exist
- I understand this is a voluntary open-source project and features are implemented as time allows