peff-uniprot-fetcher 0.1.0

Fetch UniProt protein data and generate PEFF (PSI Extended FASTA Format) files.

peff_uniprot_fetcher

Generate PEFF (PSI Extended FASTA Format) files from the UniProt REST API. Fetches protein sequences and GFF annotations (variants, PTMs, processed forms) and writes them as annotated PEFF using pefftacular.

Installation

# From source
git clone https://github.com/pgarrett-scripps/peff_uniprot_fetcher
cd peff_uniprot_fetcher
just install

CLI Usage

Fetch PEFF by organism

# Human Swiss-Prot proteome (reviewed only)
fetch-peff human.peff --organism-id 9606

# E. coli K-12
fetch-peff ecoli.peff --organism-id 83333

# Include unreviewed (TrEMBL) entries
fetch-peff human_full.peff --organism-id 9606 --unreviewed

# Custom UniProt query
fetch-peff kinases.peff --query "organism_id:9606 AND keyword:KW-0418"

# Specific accessions
fetch-peff selected.peff --accessions P12345 Q99999 O75807

# Sequences only, no annotations
fetch-peff seqs.peff --organism-id 9606 --no-variants --no-modifications --no-processed

Convert a local FASTA to PEFF

Sequences come from the local file; GFF annotations are fetched from UniProt per accession.

fasta-to-peff input.fasta output.peff

Download raw UniProt files

Download FASTA and/or GFF files for local inspection.

# Single accession
download-uniprot --accession P04637

# Full organism (both formats)
download-uniprot --organism-id 9606 --output-dir data/human

# GFF only
download-uniprot --organism-id 9606 --formats gff --output-dir data/human

Annotation flags

All fetch-peff and fasta-to-peff commands accept:

Flag	Effect
--no-variants	Exclude sequence variants (VariantSimple, VariantComplex)
--no-modifications	Exclude PTMs (ModResPsi, ModRes)
--no-processed	Exclude processed forms (Signal peptide, Chain, etc.)

Python API

from peff_uniprot_fetcher import fetch_peff, fetch_peff_to_file, fasta_to_peff, fasta_to_peff_file
from pefftacular import write_peff

# Fetch and write in one call
fetch_peff_to_file("human.peff", query="organism_id:9606 AND reviewed:true")

# Or get the data back
header, entries = fetch_peff(accessions=["P12345", "Q99999"])
write_peff(header, entries, "output.peff")

# From a local FASTA file
fasta_to_peff_file("input.fasta", "output.peff")
header, entries = fasta_to_peff("input.fasta")

PEFF annotations

The following UniProt GFF feature types are mapped to PEFF annotations:

UniProt feature	PEFF key
Natural variant, Mutagenesis, Sequence conflict	VariantSimple / VariantComplex
Alternative sequence (isoform)	VariantComplex
Modified residue	ModResPsi (with PSI-MOD accession) or ModRes
Glycosylation, Lipidation, Cross-link	ModRes
Signal peptide	Processed (PEFF:0001001)
Transit peptide	Processed (PEFF:0001002)
Propeptide	Processed (PEFF:0001003)
Chain (mature protein)	Processed (PEFF:0001004)
Peptide	Processed (PEFF:0001005)

PTM names are mapped to PSI-MOD accessions using the UniProt PTM list.

Just recipes

just download-ecoli        # download raw E. coli K-12 FASTA + GFF to data/ecoli/
just fetch-ecoli           # generate PEFF for E. coli K-12
just fasta-to-peff-ecoli   # convert downloaded E. coli FASTA to PEFF

Development

just lint      # ruff check
just format    # ruff format
just check     # lint + type check + test
just test      # pytest