origenomi 0.1.2

Trim circular overlaps, find dnaA/oriC, rotate sequences, and report.

Origami

Command-line tool that:

• Trims duplicated terminal overlaps in circular assemblies (half2 → DB(half1) via BLAST).
• Runs one BLAST per DB (dnaA and oriC) on the concatenated FASTA.
• Keeps top 3 dnaA and top 7 oriC per record (dedup by sseqid, ordered by evalue→identity→coverage→bitscore).
• Pairs dnaA–oriC via midpoint proximity (1% then 5% of record length, else closest), computes AT/GC on the oriC segment, and chooses the pair with highest AT/GC ratio (tie → higher AT%).
• Rotates so the earlier of dnaA/oriC starts the sequence (or the single site if only one found).
• Writes exactly two outputs: origami_<prefix>.fna and origami_<prefix>_report.txt.

Install

pip install -e .

Usage

Full pipeline

origami run -i genome.fna --dnaA-db /path/new_dnaA_DB --oric-db /path/DoriC_DB

Trim only

origami trim -i genome.fna

OriC only (no trim)

origami oric -i genome.fna --dnaA-db /path/new_dnaA_DB --oric-db /path/DoriC_DB

Outputs

1. origami_.fna
2. origami__report.txt
3. Temps in ./temp//, cleaned unless --keep-temp.