https://github.com/broadinstitute/g2papi
Python Client Library for the G2P Portal API
https://github.com/broadinstitute/g2papi
bioinformatics bioinformatics-tool bioinformatics-visualization isoforms protein-structure proteins sequence-alignment variant-analysis
Last synced: about 1 month ago
JSON representation
Python Client Library for the G2P Portal API
- Host: GitHub
- URL: https://github.com/broadinstitute/g2papi
- Owner: broadinstitute
- License: mit
- Created: 2024-03-26T22:10:11.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-08-14T20:06:41.000Z (about 2 months ago)
- Last Synced: 2025-08-14T22:10:39.184Z (about 2 months ago)
- Topics: bioinformatics, bioinformatics-tool, bioinformatics-visualization, isoforms, protein-structure, proteins, sequence-alignment, variant-analysis
- Language: Python
- Homepage: https://g2p.broadinstitute.org
- Size: 4.35 MB
- Stars: 12
- Watchers: 7
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# g2papi
`g2papi` is a Python library and command-line tool designed to interact with the G2P API provided by the Broad Institute. It allows users to retrieve mappings between protein isoforms, transcripts, and PDB structures for a gene, as well as protein feature tables for a gene.
Access the swagger definition and endpoints at: https://g2p.broadinstitute.org/api-docs/
## Citation
If you use g2papi in your research, please cite:
Kwon S, et al. Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures. doi: https://doi.org/10.1101/2024.01.02.573913.
## Installation
First, ensure that you have Python and pip installed on your system.
### Installing with PyPi
```
pip install g2papi
```
### Installing from source
Clone this repository to your local machine and navigate into the cloned directory:
```
git clone https://github.com/broadinstitute/g2papi.git
cd g2papi
```
To install `g2papi`, run:
```
pip install .
```
This will install the `g2papi` package and its dependencies.
## Usage
### As a Python Library
You can import `g2papi` in your Python scripts to retrieve data from the G2P API directly. Here are some examples:
Calling the G2P3D API to get the Gene-Transcript-Protein Isoform-Structure mapping
```python
import g2papi
# Get gene-transcript-protein isoform-protein structure map as a pandas dataframe
gene_transcript_protein_isoform_struct = g2papi.get_gene_transcript_protein_isoform_structure('BRCA1', 'P38398')
print(gene_transcript_protein_isoform_struct[['UniProt Isoform','Ensembl Transcript Id', 'RefSeq mRNA Id']].head())
```
Output:
```
UniProt Isoform Ensembl Transcript Id RefSeq mRNA Id
0 P38398-1(*) ENST00000357654(*) NM_001407611
1 P38398-1(*) ENST00000357654(*) NM_001407616
2 P38398-1(*) ENST00000357654(*) NM_001407624
3 P38398-1(*) ENST00000357654(*) NM_001407637
4 P38398-1(*) ENST00000357654(*) NM_001407641
```
Getting Protein Features
```python
import g2papi
# Get protein features as a pandas dataframe
protein_features = g2papi.get_protein_features('BRCA1', 'P38398')
protein_features.fillna('-', inplace=True)
print(protein_features[[
'residueId', 'AA',
'AlphaFold confidence (pLDDT)',
'Active site (UniProt)'
]].head())
```
Output:
```
residueId AA AlphaFold confidence (pLDDT) Active site (UniProt)
0 1 M 41.59 -
1 2 D 45.81 -
2 3 L 48.11 -
3 4 S 63.99 -
4 5 A 61.73 -
```
### As a Command-Line Tool
g2papi can also be used as a command-line tool to retrieve information directly to your terminal or output files.
Getting Gene-Transcript-Protein Isoform-Structure Map with the G2P3D API
```
g2papi get-gene-transcript-protein-isoform-structure-map --geneName BRCA1 --uniprotId P38398
```
Getting Protein Features
```
g2papi get-protein-features --geneName BRCA1 --uniprotId P38398
```
The above commands will print the results to your terminal. If you wish to save the output to a file, you can redirect the output:
```
g2papi get-gene-transcript-protein-isoform-structure-map --geneName BRCA1 --uniprotId P38398 > transcript_map.tsv
g2papi get-protein-features --geneName BRCA1 --uniprotId P38398 > protein_features.tsv
```
## System Requirements
The package was developed and tested on Python 3.9.12, and is designed to run on a computer that can run Python3 and has a working internet connection. The library was installed and tested on Ubuntu Linux 20.04 and Mac OSX Ventura, 13.5.1.
## Set up time (total time to set up and run: approximately 5 minutes)
Installation and execution steps run in approximately real time. 3 installation steps each run in less than 5 seconds, and execution time takes less than 5 seconds for genes with under 2000 residues.