Metadata-Version: 2.4
Name: orfmatch
Version: 0.2.2
Summary: Transfer feature annotations from a reference genome to a de novo assembled one.
Project-URL: Homepage, https://github.com/mcgilmore/orfmatch
Project-URL: Repository, https://github.com/mcgilmore/orfmatch.git
Author-email: mcgilmore <michael_gilmore@live.com>
License-Expression: GPL-3.0-only
License-File: LICENSE
Requires-Python: >=3.9
Requires-Dist: biopython<2,>=1.85
Requires-Dist: pycirclize<2,>=1.9.1
Requires-Dist: pygenomeviz<2,>=1.6.1
Requires-Dist: pyhmmer<0.12,>=0.11.1
Requires-Dist: pyrodigal<4,>=3.6.3.post1
Requires-Dist: seaborn<0.14,>=0.13.2
Requires-Dist: tqdm<5,>=4.67.1
Description-Content-Type: text/markdown

# orfmatch

Transfer feature annotations from a reference genome to a *de novo* assembled one, where the new genome sequence is from the same or a closely related strain.

## Installation

Install using pip:

`pip install orfmatch`

or from github:

`pip install git+https://github.com/mcgilmore/orfmatch.git`

## Usage

- Input is an assembly in \*.fasta format.
- Reference genome and output genome are in GenBank format (\*.gbff).

`orfmatch --input <assembly.fasta> --reference <reference.gbff> --output <output.gbff>`

### Optional

- `-e` / `--e-value`: E value cutoff for phmmer protein match search (default: `1e-25`).
- `-v` / `--variants`: Outputs matched sequences with differences from the reference to `variants.fasta` and alignment to `variants_alignment.txt`.
- `-c` / `--circle`: Produces a circle plot with features mapped between reference and assembly in SVG format.
- `-l` / `--line`: Produces a linear plot with features mapped between reference and assembly in SVG format.
- `-t` / `--threads`: Number of threads used for processing (default: `8`)
