Skip to main content

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

Project description

[![Build Status](https://travis-ci.org/MDU-PHL/ngmaster.svg?branch=master)](https://travis-ci.org/MDU-PHL/ngmaster)
[![License: GPLv2](https://img.shields.io/badge/License-GPL_2.0-blue.svg)](https://www.gnu.org/licenses/gpl-2.0)
![Python 3.6](https://img.shields.io/badge/Language-Python_3.6-steelblue.svg)

# ngmaster

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

## Synopis
```
% ngmaster.py gono.fa
ID NG-MAST POR TBPB
gono.fa 10699 6277 4
```

## Dependencies

* [Python >= 3.6](https://www.python.org/)
* [BioPython](http://biopython.org/)
* [isPcr >= v33x2](http://hgwdev.cse.ucsc.edu/~kent/src/) by Jim Kent

## Installation

### PiPy
```
pip3 install ngmaster
```
### Brew
```
brew install brewsci/bio/ngmaster # COMING SOON
```
### Conda
```
conda install -c bioconda -c conda-forge 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](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](https://www.ncbi.nlm.nih.gov/pubmed/28348871)
DOI:[10.1099/mgen.0.000076](https://doi.org/10.1099/mgen.0.000076)

## Bugs

### Software
Please submit via the [GitHub issues page](https://github.com/MDU-PHL/ngmaster/issues).

### 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](mailto:d.aanensen@imperial.ac.uk).

## Software Licence

[GPLv2](https://github.com/MDU-PHL/ngmaster/blob/master/LICENSE)

## References

* Martin et al. J Infect Dis, 2004 Apr 15; 189(8): 1497-1505.
* See also [http://www.ng-mast.net](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.


Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
ngmaster-0.5.5-py3-none-any.whl (1.0 MB) Copy SHA256 hash SHA256 Wheel py3
ngmaster-0.5.5.tar.gz (931.0 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page