Link Search Menu Expand Document

UniProt downloader is a bash shell script for downloading UniProt protein sequences to a FASTA amino acid (.faa) file. It takes a list of UniProt accession numbers as input, and then pipes each one into a curl command to download the corresponding protein. This is essentially a one-line program wrapped in a shell script to make downloading UniProt sequences easier.

Usage [-h|--help] [-p|--processors n -o|--output] -i|--input 
 This script takes a list of UniProt primary accession numbers (*.list), and 
 downloads the corresponding protein sequences from UniProt as a FASTA amino 
 acid (.faa) file.
 This list can be generated by searching UniProtKB for a desired term (e.g. 
 'taxonomy:147537' for the Saccharomycotina subphylum), selecting 'Download' 
 and 'Format: List' to download the accession numbers of the corresponding 
 	 -h | --help		 show this help text and exit 
 	 -i | --input		 the list of UniProt proteins to download 
 	 -p | --processors	 optional: set the number (n) of processors to 
 				 use (default: 1) 
 	 -o | --output		 optional: name of the output .faa file 
 				 (default: uniprot_{date}.faa) 

See also