https://github.com/srom/assembly
Fetch and process genome assembly data from NCBI.
https://github.com/srom/assembly
Last synced: 2 months ago
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Fetch and process genome assembly data from NCBI.
- Host: GitHub
- URL: https://github.com/srom/assembly
- Owner: srom
- License: mit
- Created: 2024-09-23T10:16:50.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-11-29T14:49:09.000Z (over 1 year ago)
- Last Synced: 2025-11-28T02:19:29.523Z (8 months ago)
- Language: Python
- Size: 24.1 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
Assembly
----------
Fetch and process genome assembly data from [NCBI](https://www.ncbi.nlm.nih.gov/).
## Installation
### Locally with conda
```sh
git clone https://github.com/srom/assembly.git
cd assembly
conda env create -f environment.yml
conda activate assembly
```
### Pip
PyPI package TBD.
### Conda
Conda package TBD.
## Run
### Download genomes from NCBI
Prepare text file with one assembly accession per file, e.g.:
```
GCA_018222585.1
GCF_000337575.1
GCA_016840645.1
GCA_dummy0001.1
```
Non-existent accessions (such as the last one above) are logged and reported in a file (`missing-accessions.txt`), but they won't make the execution fail and other genomes will still get downloaded.
Run command:
```sh
python -m src.fetch_assemblies -l test_data/assembly_accessions.txt -o test_data
```
### Predict coding sequences (CDS) with Prodigal (optional)
Automatically only runs on genomes without protein fasta file available. Suitable for prokaryotes or phages. [Prodigal](https://github.com/hyattpd/Prodigal) must be installed.
```sh
python -m src.postprocessing.predict_cds -i test_data
```
### Concatenate all proteins sequences in one fasta file (optional)
```sh
python -m src.postprocessing.concatenate_proteins -i test_data -o test_data/all_proteins.fasta
```
## Outputs
See example output in folder [`test_data/`](test_data), generated with [`run_test.sh`](run_test.sh).