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CoreuScan

A tool to download Core Genome MLST schemes for bacterial genomics

Installation and requirements

Requires Python 3

pip3 install git+https://github.com/kristyhoran/coreuscan.git#egg=coreuscan

Author: Kristy Horan

Main functions

  1. Find a database for a species and particular scheme
  2. Download an existing cgMLST scheme (or 7 gene MLST) from a database
usage: coreuscan.py [-h] [-s SEARCH] [-l] [-L, --list-db] [-d] [-sp SPECIES]
                    [-db DB] [-o OUTPATH] [-st SCHEMA_TYPE]

Download MLST schema

optional arguments:
  -h, --help            show this help message and exit
  -s SEARCH, --search SEARCH
                        Search for a species and scheme type. Only possible to
                        search for one species at a time. Accepted strings are
                        one of genus, first letter of genus immediately
                        followed by species (no spaces or punctuation) or
                        species only
  -l, --list            show a list species for which schema are currently
                        available of all available shema. No input required
  -L, --list-db         list all available databases
  -d, --download        Download a MLST scheme.
  -sp SPECIES, --species SPECIES
                        REQUIRED if -d selected. The species for which the
                        MLST scheme is to be downloaded.
  -db DB, --database DB
                        OPTIONAL The location of the MLST database, if known.
                        For use with, list, search and download
  -o OUTPATH, --output OUTPATH
                        OPTIONAL An output path to save the .fasta files to.
                        Default is under pwd <species>_schema/
  -st SCHEMA_TYPE, --schema_type SCHEMA_TYPE
                        The type of schema, available options are cg or trad

List databases

coreuscan.py -L
======================================================>
Databases available through CoreuScan are:
======================================================>

Core genome schemes are available from:
------------------------------------------------------->
Enterobase
cgMLST
Pasteur Institute

7 gene MLST schemes are also available from:
------------------------------------------------------->
Enterobase
pubMLST
Pasteur Institute

Find a database

coreuscan/coreuscan.py -s ecoli -st cg
======================================================>
Searching for ecoli
======================================================>
A ecoli Core Genome was found as ecoli in Enterobase

Download a scheme

coreuscan.py -d -s listeria -st cg -db Pasteur -o path_for_scheme