protmapper 0.0.29

Map protein sites to human reference sequence.

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.

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

@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}
}