This script downloads UniProtKB reference proteomes in FASTA format for a given proteome ID.
python download_reference_proteomes.py proteome_id1 proteome_id2 ...
proteome_id: The UniProtKB proteome identifier(s) to download.
The script requires Python 3 and the following packages:
- requests
- argparse
- re
To install the packages, run the following command:
pip install requests argparse re
The script downloads UniProtKB reference proteomes in batches using the UniProt REST API. Each batch contains 500 sequences, and the script will download all batches of a single proteome and concatenate them into a single FASTA file. The file will be saved in the working directory with the name proteome_id.fasta.
Download the proteomes for UP000005640 (Homo sapiens) and UP000000625 (Escherichia coli (strain K12)):
python download_reference_proteomes.py UP000005640 UP000002311
This will create two files UP000005640.fasta and UP000002311.fasta in the working directory.