# Protmapper
The Protmapper maps references to protein sites to the human reference
sequence based on UniProt, PhosphoSitePlus, and manual curation.
## Installation
### Python package
The Protmapper is a Python package that is available on PyPI and can be
installed as:
```
pip install protmapper
```
### Docker container
Alternatively, the Protmapper Docker container can be run to expose it as
a REST API as:
```
docker run -d -p 8008:8008 labsyspharm/protmapper:latest
```
## 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 linerepresents 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).
```
## Documentation
For a detailed documentation of the Protmapper, visit http://protmapper.readthedocs.io
## Funding
The development of protmapper is funded under the DARPA Automated Scientific Discovery Framework project (ARO grant W911NF018-1-0124).
## Citation
```bibtex
@article{bachman2019protmapper,
author = {Bachman, John A and Gyori, Benjamin M and Sorger, Peter K},
doi = {10.1101/822668},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
title = {{Assembling a phosphoproteomic knowledge base using ProtMapper to normalize phosphosite information from databases and text mining}},
url = {https://www.biorxiv.org/content/early/2019/11/06/822668.1},
year = {2019}
}
```
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