{
    "info": {
        "author": "Jason Kwong",
        "author_email": "kwongj@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Medical Science Apps."
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        "description": "[![Build Status](https://travis-ci.org/MDU-PHL/ngmaster.svg?branch=master)](https://travis-ci.org/MDU-PHL/ngmaster)\n[![License: GPLv2](https://img.shields.io/badge/License-GPL_2.0-blue.svg)](https://www.gnu.org/licenses/gpl-2.0)\n![Python 3.6](https://img.shields.io/badge/Language-Python_3.6-steelblue.svg)\n\n# ngmaster\n\n*In silico* multi-antigen sequence typing for *Neisseria gonorrhoeae* (NG-MAST).  \n\n## Synopis\n```\n% ngmaster.py gono.fa\nID         NG-MAST    POR    TBPB\ngono.fa    10699      6277   4\n```\n\n## Dependencies\n\n* [Python >= 3.6](https://www.python.org/)\n* [BioPython](http://biopython.org/)\n* [isPcr >= v33x2](http://hgwdev.cse.ucsc.edu/~kent/src/) by Jim Kent\n\n## Installation\n\n### PiPy\n```\npip3 install ngmaster\n```\n### Brew\n```\nbrew install brewsci/bio/ngmaster  # COMING SOON\n```\n### Conda\n```\nconda install -c bioconda -c conda-forge ngmaster  # COMING SOON\n```\n\n## Test\n\nOnce installed, you can run the following to ensure `ngmaster` is successfully working:\n\n    $ ngmaster --test\n\nIf everything works, you will see the following:\n\n```\nRunning ngmaster.py on test example (NG-MAST 10699) ...\n$ ngmaster.py test/test.fa\nID    NG-MAST    POR    TBPB\ntest.fa    10699    6277    4\n... Test successful.\n```\n\n## Usage\n\n    $ ngmaster -h\n\n    usage:\n      ngmaster [OPTIONS] <fasta1> <fasta2> <fasta3> ... <fastaN>\n\n    In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)\n\n    Please cite as:\n      Kwong JC, Goncalves da Silva A, Howden BP and Seemann T.\n      NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)\n      GitHub: https://github.com/MDU-PHL/ngmaster\n\n    positional arguments:\n      FASTA            input FASTA files eg. fasta1, fasta2, fasta3 ... fastaN\n\n    optional arguments:\n      -h, --help       show this help message and exit\n      --db DB          specify custom directory containing allele databases\n                       directory must contain database files \"POR.tfa\", \"TBPB.tfa\", and \"ng_mast.txt\"\n      --csv               output comma-separated format (CSV) rather than tab-separated\n      --printseq FILE  specify filename to save allele sequences to (default=off)\n       --updatedb       update allele database from <www.ng-mast.net>\n      --test           run test example\n      --version        show program's version number and exit\n\n\n## Quick start\n\n**To perform *in silico* NG-MAST on FASTA files:**\n\n`$ ngmaster <fasta1> <fasta2> <fasta3> ... <fastaN>`\n\nThe NG-MAST result and allele numbers are printed in tab-separated format to `stdout`.\n* If an allele is not found (ie. unable to located with primers), the allele result is \"`\u2013`\".\n* If an allele is found (ie. located with primers), but the conserved region containing the starting key motif required for sequence trimming cannot be located, the allele result is \"`no_key`\".\n* If an allele is found (ie. located with primers), but the trimmed sequence is novel, and not in the current database, the allele result is \"`new`\".\n\n**To save results to a tab-separated text file, redirect `stdout`:**\n\n`$ ngmaster <fasta1> <fasta2> <fasta3> ... <fastaN>  > results.txt`\n\n**To display results in comma-separated format, use the `--csv` option:**\n\n`$ ngmaster --csv <fasta1> <fasta2> <fasta3> ... <fastaN>`\n\n**To save sequences of the alleles to a file (eg. for uploading \"new\" sequences to [http://www.ng-mast.net](http://www.ng-mast.net/)):**\n\n`$ ngmaster --printseq [filename] <fasta1> <fasta2> <fasta3> ... <fastaN>`\n\n## Updating the allele databases\n\n**To update the allele databases from http://www.ng-mast.net :**  \n*Warning: This will overwrite the existing databases so ensure you back them up if you wish to keep them.*\n\n    $ ngmaster.py --updatedb\n\nA copy of the old database is saved just in case, but is overwritten with each subsequent   ```--updatedb```.\n\n**To update the allele databases into a different folder (ie. not the /db folder in the ngmaster directory):**\n\n    $ ngmaster.py --updatedb --db path/to/folder\n\nThis will download the database files into the folder ```path/to/folder```.\nThis can then be specified when running ngmaster using the ```--db  path/to/folder``` option.\n\n## Creating a custom allele database\n\n1. Create custom database files: `POR.tfa`, `TBPB.tfa`, `ng_mast.txt`  \n   See default `db` directory for examples.  \n   `POR.tfa` and `TBPB.tfa` contain the respective allele sequences in FASTA format.  \n   `ng_mast.txt` contains a list of NG-MAST types and the corresponding allele types.\n\n2. Place the custom database files in a folder.\n\n3. Specify the path to that custom database folder:  \n   `$ ngmaster --db [/path/to/custom/folder/] <fasta1> <fasta2> <fasta3> ... <fastaN>`\n\n## Citation\n\nKwong JC, Gon\u00e7alves da Silva A, Dyet K, Williamson DA, Stinear TP, Howden BP and Seemann T.  \n_NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeae_\n**Microbial Genomics**\n2016 Aug 25;2(8):e000076.\nPMID:[28348871](https://www.ncbi.nlm.nih.gov/pubmed/28348871)\nDOI:[10.1099/mgen.0.000076](https://doi.org/10.1099/mgen.0.000076)\n\n## Bugs\n\n### Software\nPlease submit via the [GitHub issues page](https://github.com/MDU-PHL/ngmaster/issues).  \n\n### Database\nNote that the NG-MAST databases and website are curated and hosted at the\nDepartment of Infectious Disease Epidemiology, Imperial College London.  For\nissues with the NG-MAST databases, please contact the [NG-MAST\ncurator](mailto:d.aanensen@imperial.ac.uk).\n\n## Software Licence\n\n[GPLv2](https://github.com/MDU-PHL/ngmaster/blob/master/LICENSE)\n\n## References\n\n* Martin et al. J Infect Dis, 2004 Apr 15; 189(8): 1497-1505.  \n* See also [http://www.ng-mast.net](http://www.ng-mast.net/).\n\n## Authors\n\n* Jason Kwong (@kwongjc)\n* Anders Gon\u00e7alves da Silva (@drandersgs)\n* Mark Schultz (@schultzm)\n* Torsten Seemann (@torstenseemann)\n\n## Development\n\nWhen incrementing version (i.e., minor patch), run the following:\n\n```\nbumpversion --verbose --dry-run --new-version <major.minor.patch> patch\nbumpversion --new-version <new.version.number> patch\n```\n\nThe same can be done for `minor` and `major` numbers.\n\nThis will automatically commit and tag the commit with the new version number.\nIt will also update the necessary location in the file.\n\n\n",
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