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

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# ngmaster

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

## Synopis
% gono.fa
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 # 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 on test example (NG-MAST 10699) ...
$ test/test.fa
test.fa 10699 6277 4
... Test successful.

## Usage

$ ngmaster -h

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)

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 <>
--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 [](**

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

## Updating the allele databases

**To update the allele databases from :**
*Warning: This will overwrite the existing databases so ensure you back them up if you wish to keep them.*

$ --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):**

$ --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.

## 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

## Software Licence


## References

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

## 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.

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