Download, extract, and flatten NCBI genome archive.
The NCBI genome archive allows you to download reference genomes through a web interface or through
REST API in a nice zip archive.
There is only one issue, it comes in a deep nested structure with a lot of ancillary files.
For instance, after downloading the reference genome of Rice (Oryza sativa Japonica Group) with ID GCF_034140825.1 through the web interface, selecting only the gtf file to minimize the download size, the ncbi_dataset.zip has the following structure:
ncbi_dataset.zip
├── ncbi_dataset
│ └── data
│ ├── assembly_data_report.jsonl
│ ├── dataset_catalog.json
│ ├── data_summary.tsv
│ └── GCF_034140825.1
│ └── genomic.gtf
└── README.md
That is a lot of files and folders despite requesting only the gtf file.
Typically, only the genomic fasta and gtf files are required for most analyses.
On top of that, the gtf file doesn't even have a nice file name,
having rather generic genomic.gtf.
This makes it quite laborious to integrate this easily into pipelines
since a lot of manual intervention: unpacking, sorting, perhaps even renaming, is required.
Here comes ncbi.r, a stand-alone R script with no dependencies that does this work for you.
Only up-to-date R version is required.
Just copy paste the script where you need it and run it directly with Rscript.
Alternatively, add it to your PATH and mark it as executable.
See your OS help pages on how to do that.
For instance, on my Linux machine, my home directory contains a bin folder that was added to PATH system variable. I can just copy the ncbi.r there, type:
chmod +x $HOME/bin/ncbi.r
and now I can simply type ncbi.r to run the script from anywhere.
If ncbi.r is not in your path, navigate to where you downloaded the file and type:
Rscript ncbi.r --help
This will display usage instructions.
To download, extract, and flatten the GCF_034140825.1 genome, type:
Rscript ncbi.r GCF_034140825.1
This will download the Rice reference genome and create two files in your current path:
GCF_034140825.1.fna.gz and GCF_034140825.1.gtf.gz.