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Python arguments are equivalent to long-option arguments (--arg), unless otherwise specified. Flags are True/False arguments in Python. The manual for any gget tool can be called from the command-line using the -h --help flag.

gget g2p 🧬➜🧪

Query the Genomics 2 Proteins (G2P) portal to link genes/proteins to residue-level structural and functional annotations, the gene–transcript–protein–isoform–structure map, and isoform alignments.

The per-residue feature table is rich (~140 columns), including AlphaFold pLDDT, DSSP secondary structure, accessible surface area, UniProt sites (active/binding/domain/...), PhosphoSitePlus PTMs, fpocket / af2bind / p2rank pocket predictions, intra- and inter-chain hydrogen bonds, non-bonded interactions, disulfide bonds and salt bridges (from PDB and AlphaFold), the PFES (Protein Feature Enrichment Score) sub-scores used by G2P for missense variant interpretation, and per-residue MaveDB experimental functional scores. See the g2p-bis documentation for column descriptions.

Note: this module wraps the public G2P REST API. The variant overlays shown in the portal's web UI (gnomAD, ClinVar, HGMD) are not exposed by the public API and are therefore not available via gget g2p — use the portal directly for those.

Returns: A data frame with the requested G2P information, or None if the query failed (network error, invalid arguments, or unknown gene/UniProt pair).

This module was written by Elarwei.

At least one of gene or --uniprot_id is required — the other is resolved automatically via the UniProt REST API and cached.

Arguments (at least one of gene / --uniprot_id required)
gene (positional)
Gene symbol, e.g. BRCA1.
If omitted, resolved from --uniprot_id. In this case, note that gene → UniProt accession lookup is approximate (it picks the canonical reviewed human Swiss-Prot entry only); for non-human organisms, unreviewed entries, or a specific isoform, pass --uniprot_id explicitly.

-u --uniprot_id
UniProt accession, e.g. P38398. If omitted, resolved from gene. For --resource alignment this is the canonical isoform (e.g. P01130-1) and is required (gene→UniProt lookup returns the base accession and cannot disambiguate isoforms).
Tip: find a gene's UniProt ID with gget search (to get a gene's Ensembl ID) and gget info.

Optional arguments
-r --resource
Defines the type of information to return (default: 'features'):
features: Per-residue protein feature table (~140 columns: AlphaFold pLDDT, UniProt sites, secondary structure, predicted pockets, PTMs, PFES, MaveDB scores, ...).
map: Gene → transcript → protein isoform → structure map (UniProt/Ensembl/RefSeq/PDB identifiers). The comma-joined PDB Ids column is augmented with a parsed PDB Ids List column (list[str]) for direct consumption (e.g. with gget pdb).
alignment: Residue-level sequence alignment between two isoforms (requires --isoform; --uniprot_id is the canonical isoform).

-i --isoform
Alternative isoform UniProt accession (e.g. P01130-2). Required when --resource alignment. Default: None.

--residues
Restrict the result to specific residue positions (applies to --resource features / alignment only). Command line: comma-separated list and/or inclusive ranges, e.g. 185,1775,1812 or 100-200 or 1-50,185. Python: int, list[int], range, or set[int]. Default: None (return all residues).

-o --out
Path to the file the results will be saved in, e.g. path/to/directory/results.json. Default: Standard out.
Python: save=True will save the output as a CSV in the current working directory; out="path/to/file.csv" writes to an explicit path and takes precedence over save.

Flags
-csv --csv
Command-line only. Returns results in CSV format instead of JSON.
Python: Use json=False (default) to return a data frame.

-q --quiet
Command-line only. Prevents progress information from being displayed.
Python: Use verbose=False to prevent progress information from being displayed.

Examples

# Per-residue protein features for BRCA1 (AlphaFold pLDDT, UniProt sites, ...).
# The gene symbol is optional — it can be resolved from the UniProt accession.
gget g2p -u P38398

# Python
gget.g2p(uniprot_id="P38398", resource="features")

→ Returns a data frame with one row per residue of the BRCA1 protein (UniProt P38398) and its structural/functional annotations.



# Same query, with the gene symbol passed explicitly
gget g2p BRCA1 -u P38398

# Python
gget.g2p("BRCA1", uniprot_id="P38398", resource="features")




# Symmetric: only the gene symbol — UniProt accession is resolved automatically
# (canonical reviewed human Swiss-Prot entry).
gget g2p BRCA1

# Python
gget.g2p("BRCA1")

→ Same as above. The resolved P38398 is logged and is visible in the leading uniprot_id column.



# Score only specific residue positions
gget g2p BRCA1 -u P38398 --residues 185,1775,1812

# Python
gget.g2p("BRCA1", uniprot_id="P38398", residues=[185, 1775, 1812])
gget.g2p("BRCA1", uniprot_id="P38398", residues=range(100, 200))

→ Returns only the requested residues from the per-residue feature table.



# Gene -> transcript -> isoform -> structure map (CSV)
gget g2p -u P38398 -r map --csv

# Python
gget.g2p(uniprot_id="P38398", resource="map")

→ Returns the mapping of BRCA1 to its UniProt isoforms, Ensembl/RefSeq identifiers, and PDB structures.



# Residue-level alignment between two LDLR isoforms
gget g2p -u P01130-1 -r alignment -i P01130-2

# Python
gget.g2p(uniprot_id="P01130-1", resource="alignment", isoform="P01130-2")

→ Returns the residue-level alignment between LDLR isoforms P01130-1 and P01130-2.

References

If you use gget g2p in a publication, please cite the following articles: