Metadata-Version: 2.1
Name: EnteroTyper
Version: 0.1.7
Summary: Scripts to type and compare assemblies based off of Enterobase schemes
Home-page: https://github.com/BFSSI-Bioinformatics-Lab/EnteroTyper
Author: Forest Dussault
Author-email: forest.dussault@canada.ca
License: UNKNOWN
Description: [![Build Status](https://travis-ci.org/BFSSI-Bioinformatics-Lab/EnteroTyper.svg?branch=master)](https://travis-ci.org/BFSSI-Bioinformatics-Lab/EnteroTyper)
        [![PyPI version](https://badge.fury.io/py/EnteroTyper.svg)](https://badge.fury.io/py/EnteroTyper)
        
        # EnteroTyper
        
        This is a set of scripts to type assemblies according to schemes retrieved from Enterobase.
        
        Enterobase databases can be manually retrieved with [EnterobasePull](https://github.com/bfssi-forest-dussault/EnterobasePull). Database files retrieved from Enterobase can be automatically formatted via makeblastdb by the typer script.
        
        ## Requirements
        - Python >= 3.6
        - [ncbi-blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) (makeblastdb and blastn must be in your $PATH)
        - [MUSCLE](https://www.drive5.com/muscle/) (muscle must be in your $PATH)
        
        ### Installation
        ```
        pip install EnteroTyper
        ```
        
        ## Usage
        ### Calling EnteroTyper
        ```
        Usage: enterotyper [OPTIONS] COMMAND [ARGS]...
        
          EnteroTyper is a suite of tools to type and evaluate assemblies with
          Enterobase typing schemes.
        
        Options:
          --help  Show this message and exit.
        
        Commands:
          bulk         Runs typer on many samples simultaneously
          compare      Compares sequence types across samples processed by typer
          concatenate  Concatenate sequences from report files generated by typer
          typer        Types an assembly based on a given Enterobase scheme
        ```
        
        
        ### Single-sample Usage
        ```
        Usage: enterotyper typer [OPTIONS]
        
          Types an assembly based on an Enterobase scheme
        
        Options:
          -i, --input_assembly PATH  Path to input assembly in FASTA format
                                     [required]
          -db, --database PATH       Path to your MLST database  [required]
          -o, --outdir PATH         Root directory to store all output files
                                     [required]
          --create_db                Set this flag to create the blastDB files using
                                     makeblastdb in the specified database
                                     directory.Will re-create the database files if
                                     they are already present.
          -v, --verbose              Set this flag to enable more verbose logging.
          --version                  Specify this flag to print the version and exit.
          --help                     Show this message and exit.
          ```
        
        ### Multi-sample Usage
        ```
        Usage: enterotyper bulk [OPTIONS]
        
          Runs typer on many samples simultaneously
        
        Options:
          -i, --input_dir PATH  Path to directory containing FASTA assemblies
                                [required]
          -db, --database PATH  Path to your MLST database  [required]
          -o, --outdir PATH    Root directory to store all output files  [required]
          --create_db           Set this flag to create the blastDB files using
                                makeblastdb in the specified database directory.Will
                                re-create the database files if they are already
                                present.
          -v, --verbose         Set this flag to enable more verbose logging.
          --version             Specify this flag to print the version and exit.
          --help                Show this message and exit.
        ```
        
        ### Sequence Concatenation
        ```
        Usage: enterotyper concatenate [OPTIONS] [TARGETS]...
        
          Takes a list of target *.BLASTn_Detailed_Report.tsv files, followed by
          several options. Extracts sequences from the BLASTn report files as FASTA
          files, aligns them all with MUSCLE, and then concatenates all sequences
          into a single FASTA.
        
        Options:
          -o, --outdir PATH     Root directory to store all output files  [required]
          -db, --database PATH  Path to your MLST database  [required]
          -v, --verbose         Set this flag to enable more verbose logging.
          --help                Show this message and exit.
        ```
        
        ### Sequence Comparison
        ```
        Usage: enterotyper compare [OPTIONS] [TARGETS]...
        
          Takes a list of target *.cgMLST_Allele_Report.tsv files as input.
          Number of mismatches will be indicated in output files -
          a zero means no mismatches between types.
        
        Options:
          -o, --outdir PATH  Root directory to store all output files  [required]
          -v, --verbose       Set this flag to enable more verbose logging.
          --help              Show this message and exit.
        ```
Platform: UNKNOWN
Requires-Python: ~=3.6
Description-Content-Type: text/markdown
