| layout | title | parent |
|---|---|---|
default |
UniProt downloader |
3. Scripts |
UniProt_downloader.sh 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.
UniProt_downloader.sh [-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
results.
arguments:
-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)