Metadata-Version: 2.1
Name: protmapper
Version: 0.0.21
Summary: Map protein sites to human reference sequence.
Home-page: https://github.com/indralab/protmapper
Author: John A. Bachman
Author-email: john_bachman@hms.harvard.edu
License: UNKNOWN
Description: # 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).
        
Keywords: protein,proteomics,sequence,alignment,assembly,post-translational,modification
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
Provides-Extra: rest_api
