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        "author": "John A. Bachman",
        "author_email": "john_bachman@hms.harvard.edu",
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            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# Protmapper\nThe Protmapper maps references to protein sites to the human reference\nsequence based on UniProt, PhosphoSitePlus, and manual curation.\n\n\n## Installation\n\n### Python package\nThe Protmapper is a Python package that is available on PyPI and can be\ninstalled as:\n\n```\npip install protmapper\n```\n\n### Docker container\nAlternatively, the Protmapper Docker container can be run to expose it as\na REST API as:\n\n```\ndocker run -d -p 8008:8008 labsyspharm/protmapper:latest\n```\n\n## Command line interface\nIn addition to supporting usage via a Python API and a REST service,\nProtmapper also provides a command line interface that can be used as follows.\n\n```bash\nRun Protmapper on a list of proteins with residues and sites provided in a\ntext file.\n\npositional arguments:\n  input                 Path to an input file. The input file is a text file\n                        in which each row consists of four comma separated\n                        values, with the first element being a protein ID, the\n                        second, the namespace in which that ID is valid\n                        (uniprot or hgnc),third, an amino acid represented as\n                        a single capital letter, and fourth, a site position\n                        on the protein.\n  output                Path to the output file to be generated. Each line of\n                        the output file corresponds to a line in the input\n                        file. Each linerepresents a mapped site produced by\n                        Protmapper.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --peptide             If given, the third element of each row of the input\n                        file is a peptide (amino acid sequence) rather than a\n                        single amino acid residue. In this case, peptide-\n                        oriented mappings are applied. In this mode the\n                        following boolean arguments are ignored.\n  --no_methionine_offset\n                        If given, will not check for off-by-one errors in site\n                        position (possibly) attributable to site numbering\n                        from mature proteins after cleavage of the initial\n                        methionine.\n  --no_orthology_mapping\n                        If given, will not check sequence positions for known\n                        modification sites in mouse or rat sequences (based on\n                        PhosphoSitePlus data).\n  --no_isoform_mapping  If given, will not check sequence positions for known\n                        modifications in other human isoforms of the protein\n                        (based on PhosphoSitePlus data).\n\n```\n\n## Documentation\nFor a detailed documentation of the Protmapper, visit http://protmapper.readthedocs.io\n\n## Funding\nThe development of protmapper is funded under the DARPA Automated Scientific Discovery Framework project (ARO grant W911NF018-1-0124).\n\n\n",
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        "name": "protmapper",
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