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In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)

Project description

Build Status License: GPLv2 Python 3.6 DOI:10.1099/mgen.0.000076

ngmaster

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST).

Synopsis

% ngmaster gono.fa
ID         NG-MAST    POR    TBPB
gono.fa    10699      6277   4

Dependencies

Installation

PiPy

pip3 install ngmaster

Brew

brew install brewsci/bio/ngmaster

Conda

conda install -c conda-forge -c bioconda -c defaults ngmaster  # COMING SOON

Test

Once installed, you can run the following to ensure ngmaster is successfully working:

$ ngmaster --test

If everything works, you will see the following:

Running ngmaster.py on test example (NG-MAST 10699) ...
$ ngmaster.py test/test.fa
ID    NG-MAST    POR    TBPB
test.fa    10699    6277    4
... Test successful.

Usage

$ ngmaster -h

usage:
  ngmaster [OPTIONS] <fasta1> <fasta2> <fasta3> ... <fastaN>

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)

Please cite as:
  Kwong JC, Goncalves da Silva A, Howden BP and Seemann T.
  NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
  GitHub: https://github.com/MDU-PHL/ngmaster

positional arguments:
  FASTA            input FASTA files eg. fasta1, fasta2, fasta3 ... fastaN

optional arguments:
  -h, --help       show this help message and exit
  --db DB          specify custom directory containing allele databases
                   directory must contain database files "POR.tfa", "TBPB.tfa", and "ng_mast.txt"
  --csv               output comma-separated format (CSV) rather than tab-separated
  --printseq FILE  specify filename to save allele sequences to (default=off)
   --updatedb       update allele database from <www.ng-mast.net>
  --test           run test example
  --version        show program's version number and exit

Quick start

To perform in silico NG-MAST on FASTA files:

$ ngmaster <fasta1> <fasta2> <fasta3> ... <fastaN>

The NG-MAST result and allele numbers are printed in tab-separated format to stdout.

  • If an allele is not found (ie. unable to located with primers), the allele result is "".
  • 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".
  • 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".

To save results to a tab-separated text file, redirect stdout:

$ ngmaster <fasta1> <fasta2> <fasta3> ... <fastaN> > results.txt

To display results in comma-separated format, use the --csv option:

$ ngmaster --csv <fasta1> <fasta2> <fasta3> ... <fastaN>

To save sequences of the alleles to a file (eg. for uploading "new" sequences to http://www.ng-mast.net):

$ ngmaster --printseq [filename] <fasta1> <fasta2> <fasta3> ... <fastaN>

Updating the allele databases

To update the allele databases from http://www.ng-mast.net :
Warning: This will overwrite the existing databases so ensure you back them up if you wish to keep them.

$ ngmaster.py --updatedb

A copy of the old database is saved just in case, but is overwritten with each subsequent --updatedb.

To update the allele databases into a different folder (ie. not the /db folder in the ngmaster directory):

$ ngmaster.py --updatedb --db path/to/folder

This will download the database files into the folder path/to/folder. This can then be specified when running ngmaster using the --db path/to/folder option.

Creating a custom allele database

  1. Create custom database files: POR.tfa, TBPB.tfa, ng_mast.txt
    See default db directory for examples.
    POR.tfa and TBPB.tfa contain the respective allele sequences in FASTA format.
    ng_mast.txt contains a list of NG-MAST types and the corresponding allele types.

  2. Place the custom database files in a folder.

  3. Specify the path to that custom database folder:
    $ ngmaster --db [/path/to/custom/folder/] <fasta1> <fasta2> <fasta3> ... <fastaN>

Citation

Kwong JC, Gonçalves da Silva A, Dyet K, Williamson DA, Stinear TP, Howden BP and Seemann T.
NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeae Microbial Genomics 2016 Aug 25;2(8):e000076. PMID:28348871 DOI:10.1099/mgen.0.000076

Bugs

Software

Please submit via the GitHub issues page.

Database

Note that the NG-MAST databases and website are curated and hosted at the Department of Infectious Disease Epidemiology, Imperial College London. For issues with the NG-MAST databases, please contact the NG-MAST curator.

Software Licence

GPLv2

References

Authors

  • Jason Kwong (@kwongjc)
  • Anders Gonçalves da Silva (@drandersgs)
  • Mark Schultz (@schultzm)
  • Torsten Seemann (@torstenseemann)

Development

When incrementing version (i.e., minor patch), run the following:

bumpversion --verbose --dry-run --new-version <major.minor.patch> patch
bumpversion --new-version <new.version.number> patch

The same can be done for minor and major numbers.

This will automatically commit and tag the commit with the new version number. It will also update the necessary location in the file.

Pushing to pypi

Must be uploaded to maintainer's account.

bumpversion --new-version <new.version.number> <patch|minor|major>
git push
# create distribution
python3 setup.py sdist bdist_wheel
# run some checkes
twine check dist/*
# upload to test pypi to see if everything works
twine upload --repository-url https://test.pypi.org/legacy/ dist/*
# upload to pypi
twine upload dist/*

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