Package: meningotype
meningotypeIn silicotyping ofNeisseria meningitidiscontigsSerotypingMLSTFinetyping (porA,fetA,porB)Bexsero antigen sequence typing (BAST) (fHbp,NHBA,NadA,PorA)Quick start# install
$ pip install git+https://github.com/MDU-PHL/meningotype.git

# just serotype
$ meningotype NMA.fasta

SAMPLE_ID  SEROGROUP  ctrA    MLST    PorA    FetA    PorB    fHbp    NHBA    NadA    BAST
NMA.fasta  A          ctrA    -       -       -       -       -       -       -       -

# include all genotypes
$ meningotype --all NMA.fasta

SAMPLE_ID  SEROGROUP  ctrA    MLST    PorA       FetA    PorB            fHbp    NHBA    NadA    BAST
NMA.fasta  A          ctrA    4       7,13-1     F1-5    NEIS2020_28     5       29      0       639

# type lots of files at once
$ meningotype --all *.fna

SAMPLE_ID  SEROGROUP  ctrA    MLST    PorA       FetA    PorB            fHbp    NHBA    NadA    BAST
A.fna      A          ctrA    4       7,13-1     F1-5    NEIS2020_28     5       29      0       639
B.fna      B          ctrA    8       5-2,10-1   F3-6    NEIS2020_12     16      20      8       150
C.fna      C          ctrA    177     21,26-2    F1-5    NEIS2020_3      17      101     9       118
W.fna      W          ctrA    11      5,2        F1-1    NEIS2020_244    623     29      6       141
X.fna      X          ctrA    181     5-1,10-1   F4-23   NEIS2020_509    391     358     0       -
Y.fna      Y          ctrA    23      5-2,10-1   F4-1    NEIS2020_67     25      7       0       228InstallationDependenciesPython >=3.6.xBioPythonisPcr v33NCBI BLAST+ >= 2.4mlstThe simplest way to install dependencies is to use the Brew (MacOS) or
Linuxbrew (Linux) packaging system.$ brew tap brewsci/bio
$ brew install ispcr blast mlstInstallingThe easiest way of installingmeningotypeis usingpip:$ pip install --user git+https://github.com/MDU-PHL/meningotype.gitThe--useroption will install the package locally, rather than in the globalpythondirectory.Thus, by default, this will install the package in$HOME/.local/, and the executable in$HOME/.local/bin/.
To install the executable in a custom location (e.g.,$HOME/bin), use the following:$ pip install --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/meningotype.gitTo upgrade to a newer version:$ pip install --upgrade --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/meningotype.gitTestingOnce installed, you can run the following to ensuremeningotypeis successfully working:$ meningotype.py --testIf everything works, you will see the following:$ meningotype.py --test
Running meningotype.py on test examples ... 
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID	SEROGROUP	ctrA	MLST	PorA	FetA	PorB	fHbp	NHBA	NadA	BAST
meningotype/test/A.fna	A	ctrA	-	-	-	-	-	-	-	-
meningotype/test/B.fna	B	ctrA	-	-	-	-	-	-	-	-
meningotype/test/C.fna	C	ctrA	-	-	-	-	-	-	-	-
meningotype/test/W.fna	W	ctrA	-	-	-	-	-	-	-	-
meningotype/test/X.fna	X	ctrA	-	-	-	-	-	-	-	-
meningotype/test/Y.fna	Y	ctrA	-	-	-	-	-	-	-	-or to check finetyping:$ meningotype.py --test --finetype
Running meningotype.py on test examples ... 
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID	SEROGROUP	ctrA	MLST	PorA	        FetA	PorB	fHbp	NHBA	NadA	BAST
meningotype/test/A.fna	A	ctrA	-	7,13-1		F1-5	-	-	-	-	-
meningotype/test/B.fna	B	ctrA	-	5-2,10-1	F3-6	-	-	-	-	-
meningotype/test/C.fna	C	ctrA	-	21,26-2		F1-5	-	-	-	-	-
meningotype/test/W.fna	W	ctrA	-	5,2		F1-1	-	-	-	-	-
meningotype/test/X.fna	X	ctrA	-	5-1,10-1	F4-23	-	-	-	-	-
meningotype/test/Y.fna	Y	ctrA	-	5-2,10-1	F4-1	-	-	-	-	-or to check finetyping and Bexsero antigen sequence typing:$ meningotype.py --test --all
Running meningotype.py on test examples ... 
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID	SEROGROUP	ctrA	MLST	PorA		FetA	PorB		fHbp	NHBA	NadA	BAST
meningotype/test/A.fna	A	ctrA	4	7,13-1		F1-5	NEIS2020_28		5	29	0	639
meningotype/test/B.fna	B	ctrA	8	5-2,10-1	F3-6	NEIS2020_12		16	20	8	150
meningotype/test/C.fna	C	ctrA	177	21,26-2		F1-5	NEIS2020_3		17	101	9	118
meningotype/test/W.fna	W	ctrA	11	5,2		F1-1	NEIS2020_244	623	29	6	141
meningotype/test/X.fna	X	ctrA	181	5-1,10-1	F4-23	NEIS2020_509	391	358	0	-
meningotype/test/Y.fna	Y	ctrA	23	5-2,10-1	F4-1	NEIS2020_67		25	7	0	228Usage$ meningotype.py -h
usage: 
  meningotype.py [OPTIONS] <fasta1> <fasta2> <fasta3> ... <fastaN>

In silico typing for Neisseria meningitidis
Default: Serotyping, MLST and ctrA PCR

PCR Serotyping Ref: Mothershed et al, J Clin Microbiol 2004; 42(1): 320-328
PorA and FetA typing Ref: Jolley et al, FEMS Microbiol Rev 2007; 31: 89-96
Bexsero antigen sequence typing (BAST) Ref: Brehony et al, Vaccine 2016; 34(39): 4690-4697
See also http://www.neisseria.org/nm/typing/

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

optional arguments:
  -h, --help  show this help message and exit
  --finetype  perform porA and fetA fine typing (default=off)
  --porB      perform porB sequence typing (NEIS2020) (default=off)
  --bast      perform Bexsero antigen sequence typing (BAST) (default=off)
  --mlst      perform MLST (default=off)
  --all       perform MLST, porA, fetA, porB, BAST typing (default=off)
  --db DB     specify custom directory containing allele databases for porA/fetA typing
              directory must contain database files: "FetA_VR.fas", "PorA_VR1.fas", "PorA_VR2.fas"
              for Bexsero typing: "fHbp_peptide.fas", "NHBA_peptide.fas", "NadA_peptide.fas", "BASTalleles.txt"
  --printseq  save porA/fetA or BAST allele sequences to file (default=off)
  --updatedb  update allele database from <pubmlst.org>
  --test      run test example
  --version   show program's version number and exitExamplesTo performin silicoserotyping on FASTA files:$ meningotype <fasta1> <fasta2> <fasta3> ... <fastaN>`The serotypes are printed in tab-separated format tostdout.
To save results to a tab-separated text file, redirectstdout:$ meningotype <fasta1> <fasta2> <fasta3> ... <fastaN>  > results.txtTo performin silicoserotyping AND finetyping of the porA and fetA genes:$ meningotype --finetype <fasta1> <fasta2> <fasta3> ... <fastaN>To save finetyping sequences of the alleles to a file (eg. for uploading
"new" sequences tohttp://pubmlst.org/neisseria/):$ meningotype --finetype --printseq <fasta1> <fasta2> <fasta3> ... <fastaN>These are placed into a folder calledprintseqin the current directory.Updating the allele databasesTo update the allele databases fromhttp://pubmlst.org/neisseria/$ meningotype.py --updatedbA copy of the original database is saved to*.oldjust in case,
but is overwritten with each subsequent--updatedb.Ensure you back up your old databases if you wish to keep them.CitationKwong JC, Gonçalves da Silva A, Stinear TP, Howden BP,  Seemann T.meningotype:in silicotyping forNeisseria meningitidis.GitHubhttps://github.com/MDU-PHL/meningotypeBugsSoftware - submit via theGitHub issues page.Database - contact thepubmlst curatorSoftware LicenceGPL3AuthorsJason Kwong (@kwongjc)Anders Gonçalves da Silva (@drandersg)Torsten Seemann (@torstenseemann)ReferencesPubMLST Neisseria Database.Mothershed et al. J Clin Microbiol. 2004; 42(1):320-328.Jolley et al. FEMS Microbiol Rev. 2007; 31:89-96.Brehony et al. Vaccine. 2016; 34(39):4690-4697.Bambini et al. PLoS One. 2013; 8(5):e65043.