Metadata-Version: 2.1
Name: meningotype
Version: 0.8.4
Summary: In silico serotyping and finetyping (porA and fetA) of Neisseria meningitidis
Home-page: https://github.com/MDU-PHL/meningotype
Author: Jason Kwong
Author-email: kwongj@gmail.com
License: GPLv3
Description: # meningotype
        
        *In silico* typing of *Neisseria meningitidis* contigs
        - Serotyping
        - MLST  
        - Finetyping (*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       228
        ```
        
        ## Installation
        
        ### Dependencies
        
        * [Python >=3.6.x](https://www.python.org/)
        * [BioPython](http://biopython.org/)
        * [isPcr v33](http://hgwdev.cse.ucsc.edu/~kent/src/)
        * [NCBI BLAST+ >= 2.4](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
        * [mlst](https://github.com/tseemann/mlst)
        
        The simplest way to install dependencies is to use the Brew (MacOS) or
        Linuxbrew (Linux) packaging system. 
        
        ```
        $ brew tap brewsci/bio
        $ brew install ispcr blast mlst
        ```
        
        ### Installing
        
        The easiest way of installing `meningotype` is using `pip`:
        ```
        $ pip install --user git+https://github.com/MDU-PHL/meningotype.git
        ```
         
        The `--user` option will install the package locally, rather than in the global `python` directory. 
        
        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.git
        ```
        
        To upgrade to a newer version: 
        ```
        $ pip install --upgrade --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/meningotype.git
        ```
        
        ### Testing
        
        Once installed, you can run the following to ensure `meningotype` is successfully working:
        
            $ meningotype.py --test
        
        If 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	228
        ```
        
        ## Usage
        
        ```
        $ 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 exit
        ```
        
        ## Examples
        
        To perform *in silico* serotyping on FASTA files:
        
        	$ meningotype <fasta1> <fasta2> <fasta3> ... <fastaN>`
        
        The serotypes are printed in tab-separated format to `stdout`.
        To save results to a tab-separated text file, redirect `stdout`:
        
        	$ meningotype <fasta1> <fasta2> <fasta3> ... <fastaN>  > results.txt
        
        To perform *in silico* serotyping 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 to [http://pubmlst.org/neisseria/](http://pubmlst.org/neisseria/)):
        
        	$ meningotype --finetype --printseq <fasta1> <fasta2> <fasta3> ... <fastaN>
        
        These are placed into a folder called `printseq` in the current directory.
        
        
        ## Updating the allele databases
        
        To update the allele databases from http://pubmlst.org/neisseria/
        
        	$ meningotype.py --updatedb
        
        A copy of the original database is saved to `*.old` just in case, 
        but is overwritten with each subsequent `--updatedb`.
        *Ensure you back up your old databases if you wish to keep them.*
        
        ## Citation
        
        Kwong JC, Gonçalves da Silva A, Stinear TP, Howden BP,  Seemann T.  
        ***meningotype*: *in silico* typing for *Neisseria meningitidis*.**  
        GitHub https://github.com/MDU-PHL/meningotype
        
        ## Bugs
        
        * Software - submit via the [GitHub issues page](https://github.com/MDU-PHL/meningotype/issues).  
        * Database - contact the [pubmlst curator](mailto:keith.jolley@zoo.ox.ac.uk)
        
        ## Software Licence
        
        [GPL3](https://github.com/MDU-PHL/meningotype/blob/master/LICENSE)
        
        ## Authors
        
        * Jason Kwong (@kwongjc)
        * Anders Gonçalves da Silva (@drandersg)
        * Torsten Seemann (@torstenseemann)
        
        ## References
        
        * [PubMLST Neisseria Database](https://pubmlst.org/neisseria/).  
        * [Mothershed et al. J Clin Microbiol. 2004; 42(1):320-328.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC321732/)
        * [Jolley et al. FEMS Microbiol Rev. 2007; 31:89-96.](http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6976.2006.00057.x/full)  
        * [Brehony et al. Vaccine. 2016; 34(39):4690-4697.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012890/)
        * [Bambini et al. PLoS One. 2013; 8(5):e65043.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065043)
        
        
Keywords: microbial genomics Neisseria sequence typing
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Intended Audience :: Science/Research
Description-Content-Type: text/markdown
