kristyhoran / coreuscan

A tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA

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

coreuscan's Issues

#egg=coreuscan problem

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

Anything after the hash is a comment
Do you need to quote it?

Error from command in documentation

I tried running coreuscan.py -d -s listeria -st cg -db Pasteur -o path_for_scheme exactly as listed in the documentation and got the following error:
======================================================>
Searching for listeria
======================================================>
The cache does not yet exist. Please wait.....
Requesting data from Enterobase @ enterobase.warwick.ac.uk
404 Client Error: Not Found for url: http://enterobase.warwick.ac.uk/schemes/Salmonella.cgMLSTv4/

Any assistance you could provide to correct this would be greatly appreciated.

coreuscan not coreuscan.py

When you pip install it is coreuscan - no .py extension.

Add documentation

Add installation and workflow

404 Client Error: Not Found for url

Hello,

When I try and run coreuscan --download --database enterobase -s senterica -st cg I get the following error message:

404 Client Error: Not Found for url: http://enterobase.warwick.ac.uk/schemes/Salmonella.cgMLSTv4/

It looks like Enterobase doesn't have a version 4, only a version 2. Is there a way to give coreuscan the complete path?

Thanks!