In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
Project description
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
- Python >= 3.6
- BioPython
- isPcr >= v33x2 by Jim Kent
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
-
Create custom database files:
POR.tfa
,TBPB.tfa
,ng_mast.txt
See defaultdb
directory for examples.
POR.tfa
andTBPB.tfa
contain the respective allele sequences in FASTA format.
ng_mast.txt
contains a list of NG-MAST types and the corresponding allele types. -
Place the custom database files in a folder.
-
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
References
- Martin et al. J Infect Dis, 2004 Apr 15; 189(8): 1497-1505.
- See also http://www.ng-mast.net.
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/*
Project details
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