https://github.com/gyorilab/protmapper
Map amino acid sites of post-translational modifications from models or data to reference positions.
https://github.com/gyorilab/protmapper
Last synced: 30 days ago
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Map amino acid sites of post-translational modifications from models or data to reference positions.
- Host: GitHub
- URL: https://github.com/gyorilab/protmapper
- Owner: gyorilab
- License: bsd-2-clause
- Created: 2018-12-11T18:21:51.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2024-06-26T15:16:26.000Z (11 months ago)
- Last Synced: 2025-03-30T01:36:40.684Z (about 2 months ago)
- Language: Python
- Size: 426 KB
- Stars: 7
- Watchers: 3
- Forks: 7
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Protmapper
The Protmapper maps protein sites to the human reference
sequence based on UniProt, PhosphoSitePlus, and manual curation.
## Installation and usage
### Python package
The Protmapper is a Python package that is available on PyPI and can be
installed as:
```bash
pip install protmapper
```
### Docker container
Protmapper can be run as a local service via a Docker container exposing a
REST API as:
```bash
docker run -d -p 8008:8008 gyorilab/protmapper:latest
```
Example: once the container is running, you can send requests to the REST API
```bash
curl -X POST -H "Content-Type: application/json" -d '{"site_list": [["P28482", "uniprot", "T", "184"]]}' http://localhost:8008/map_sitelist_to_human_ref
```
which is equivalent to the following Python code using the `requests` package
```python
import requests
url = 'http://localhost:8008/map_sitelist_to_human_ref'
data = {'site_list': [['P28482', 'uniprot', 'T', '184']]}
response = requests.post(url, json=data)
print(response.json())
```
### Command line interface
In addition to supporting usage via a Python API and a REST service,
Protmapper also provides a command line interface that can be used as follows.
```bash
Run Protmapper on a list of proteins with residues and sites provided in a
text file.
positional arguments:
input Path to an input file. The input file is a text file
in which each row consists of four comma separated
values, with the first element being a protein ID, the
second, the namespace in which that ID is valid
(uniprot or hgnc),third, an amino acid represented as
a single capital letter, and fourth, a site position
on the protein.
output Path to the output file to be generated. Each line of
the output file corresponds to a line in the input
file. Each line represents a mapped site produced by
Protmapper.
optional arguments:
-h, --help show this help message and exit
--peptide If given, the third element of each row of the input
file is a peptide (amino acid sequence) rather than a
single amino acid residue. In this case, peptide-
oriented mappings are applied. In this mode the
following boolean arguments are ignored.
--no_methionine_offset
If given, will not check for off-by-one errors in site
position (possibly) attributable to site numbering
from mature proteins after cleavage of the initial
methionine.
--no_orthology_mapping
If given, will not check sequence positions for known
modification sites in mouse or rat sequences (based on
PhosphoSitePlus data).
--no_isoform_mapping If given, will not check sequence positions for known
modifications in other human isoforms of the protein
(based on PhosphoSitePlus data).
```
Example: the sample file [cli_input.csv](https://raw.githubusercontent.com/gyorilab/protmapper/master/protmapper/tests/cli_input.csv)
has the following content
```csv
MAPK1,hgnc,T,183
MAPK1,hgnc,T,184
MAPK1,hgnc,T,185
MAPK1,hgnc,T,186
```
By running the following command
```bash
protmapper cli_input.csv output.csv
```
we get `output.csv` which has the following content
```csv
up_id,error_code,valid,orig_res,orig_pos,mapped_id,mapped_res,mapped_pos,description,gene_name
P28482,,False,T,183,P28482,T,185,INFERRED_MOUSE_SITE,MAPK1
P28482,,False,T,184,P28482,T,185,INFERRED_METHIONINE_CLEAVAGE,MAPK1
P28482,,True,T,185,,,,VALID,MAPK1
P28482,,False,T,186,,,,NO_MAPPING_FOUND,MAPK1
```
## Documentation
For a detailed documentation of the Protmapper, visit http://protmapper.readthedocs.io
## Funding
The development of Protmapper is funded under the DARPA grants W911NF018-1-0124
and HR00112220036.
## Citation
```bibtex
@article{bachman2022protmapper,
author = {Bachman, John A and Sorger, Peter K and Gyori, Benjamin M},
doi = {10.1101/822668},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
title = {{Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining}},
url = {https://www.biorxiv.org/content/10.1101/822668v4},
year = {2022}
}
```