[Feature]: Add support for circular sequences

[apcamargo]

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

[Ffloriel]

Thanks for looking into the project. Added in v0.2.0

[apcamargo]

Thanks, @Ffloriel. How does your implementation work? Does it make a circular graph?

[apcamargo]

Just a note: --circular is not working on its own, you need to pass --circular true.