https://github.com/mansanlab/alphafoldfetch
A tool for downloading AlphaFold structures using UniProt IDs or FASTA files
https://github.com/mansanlab/alphafoldfetch
ai alphafold bioinformatics computational-biology ml proteomics
Last synced: 3 months ago
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A tool for downloading AlphaFold structures using UniProt IDs or FASTA files
- Host: GitHub
- URL: https://github.com/mansanlab/alphafoldfetch
- Owner: mansanlab
- License: mit
- Created: 2024-10-27T02:43:53.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2026-03-24T05:15:01.000Z (4 months ago)
- Last Synced: 2026-03-25T06:22:44.766Z (3 months ago)
- Topics: ai, alphafold, bioinformatics, computational-biology, ml, proteomics
- Language: Python
- Homepage: https://mansanlab.github.io/alphafoldfetch/
- Size: 2.68 MB
- Stars: 6
- Watchers: 1
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
- Authors: AUTHORS.md
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README
# AlphaFoldFetch
AlphaFoldFetch is a command-line tool for downloading AlphaFold structure files from UniProt IDs and UniProt FASTA files.
It is meant for fast batch workflows:
- download one or many structure in one command
- choose any combination of PDB, CIF, or gzipped outputs
- tune concurrency for larger downloads
## Install
Run it without installing:
```bash
uvx --from AlphaFoldFetch affetch P11388
```
Install the CLI with `uv`:
```bash
uv tool install AlphaFoldFetch
```
## CLI Summary
```bash
affetch [OPTIONS] UNIPROT...
```
Arguments:
- `UNIPROT...`: UniProt IDs, FASTA files, or `-` for stdin
Options:
- `--output`, `-o`: output directory
- `--file-type`, `-f`: any combination of `p`, `c`, and `z`
- `--model`, `-m`: AlphaFold model version `1` through `6`
- `--n-sync`: concurrent download requests
- `--n-save`: file writes submitted per batch
## Input Rules
AlphaFoldFetch accepts:
- raw UniProt accessions like `P11388`
- text that contains a valid UniProt accession
- FASTA files ending in `.fasta`, `.fas`, `.fa`, or `.faa`
- `-` to read whitespace-separated input from stdin
FASTA parsing only keeps validated UniProt IDs from header lines.
## Output Rules
The default file-type value is `pcz`, which means:
- `p`: PDB output
- `c`: CIF output
- `z`: gzip compression
So the default behavior downloads both PDB and CIF files as gzip outputs.
### Examples
Single AlphaFold structure
```bash
affetch P11388
```
Multiple AlphaFold structures
```bash
affetch P11388 Q01320 P41516
```
Structures from a single UniProt FASTA file
```bash
affetch UP000005640_9606.fasta
```
Multiple UniProt FASTA files
```bash
affetch UP000007305_4577.fasta UP000005640_9606.fasta UP000000625_83333.fasta
```
*First obtain these FASTA files from UniProt*
Multiple custom FASTA files
```bash
affetch plant_pgks.fasta mammalian_pgks.fasta bacterial_pgks.fasta
```
*Input files must be in the UniProt FASTA file format*
Unzipped PDB file
```bash
affetch -f p P11388
```
*Default will dowload zipped PDB and CIF files for all entries*
Redirect output to a directory
```bash
mkdir human_top2a && affetch -o ./human_top2a P11388
```
EBI AlphaFold Download data - Search Results CSV File
```bash
tail -n +2 results-csv.csv | while IFS='-' read -r f1 f2 f3; do echo $f2; done | affetch -
```
Don't know the UniProt ID? Use [getSequence] and pipe into `affetch`
```bash
getseq human top2a, mouse top2a, rat top2a | affetch -
```
*Pipe input arguments must be indicated with a dash `-`*
For more information, read the [docs](https://mansanlab.github.io/alphafoldfetch/)
## Credits
Inspired by [getSequence](https://github.com/alexholehouse/getSequence).