ngmaster 1.0.0

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

ngmaster

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST) and Neisseria gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR).

Synopsis

ngmaster gono.fa
FILE	SCHEME	    NG-MAST/NG-STAR	porB_NG-MAST	tbpB	penA	mtrR	porB_NG-STAR	ponA	gyrA	parC	23S
gono.fa	ngmaSTar    4186/231            2569            241     23      42      100             100     10      2       100

Dependencies

• Python >= 3.7
• BioPython
• mlst

Installation

PiPy

# TODO how to integrate mlst dependency
pip3 install ngmaster

Brew

# TODO how to integrate mlst dependency
brew install brewsci/bio/ngmaster

Conda

conda install -c bioconda ngmaster

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 4186 / NG-STAR 231) ...
FILE	SCHEME	    NG-MAST/NG-STAR	porB_NG-MAST	tbpB	penA	mtrR	porB_NG-STAR	ponA	gyrA	parC	23S
test.fa	ngmaSTar    4186/231            2569            241     23      42      100             100     10      2       100
... Test successful.

Usage

ngmaster -h

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

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
and Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR)

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 sequence files (.tfa) and allele profile files (ngmast.txt / ngstar.txt)
                   in mlst format (see <https://github.com/tseemann/mlst#adding-a-new-scheme>)
  --csv            output comma-separated format (CSV) rather than tab-separated
  --printseq FILE  specify filename to save allele sequences to
  --minid MINID    DNA percent identity of full allele to consider 'similar' [~]
  --mincov MINCOV  DNA percent coverage to report partial allele at [?]
  --updatedb       update NG-MAST and NG-STAR allele databases from <https://rest.pubmlst.org/db/pubmlst_neisseria_seqdef>
  --assumeyes      assume you are certain you wish to update db
  --test           run test example
  --comments       include NG-STAR comments for each allele in output
  --version        show program's version number and exit

Quick start

To perform in silico NG-MAST and NG-STAR typing on FASTA files:

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

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

• ngmaster reports alleles according to the same rules that are implemented in mlst.
• mlst's arguments --minid and --mincov are available directly in ngmaster
• For each allele n:

Symbol	Meaning	Length	Identity
n	exact intact allele	100%	100%
~n	novel full length allele similar to n	100%	≥ --minid
n?	partial match to known allele	≥ --mincov	≥ --minid
-	allele missing	< --mincov	< --minid
n,m	multiple alleles

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 PubMLST):

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

This will create two files:

1. NGMAST__filename
2. NGSTAR__filename

Updating the allele databases

To update the allele databases from PubMLST:
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

To create a custom allele database please follow the instructions for creating a custom mlst database described here. Usually, this should not be necessary, simply run ngmaster --update to update to the latest NG-MAST and NG-STAR schemes from PubMLST.

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

Please submit via the GitHub issues page.

Software Licence

GPLv2

References

• Martin et al. J Infect Dis, 2004 Apr 15; 189(8): 1497-1505.
• Demczuk et al. J Clin Microbiol, 2017 May; 55(5): 1454-1468
• See also PubMLST.

Authors

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

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/*