Master:

Dev:

Installation

git clone --recursive git@github.com:Phelimb/atlas.git    
python setup.py install

OR

(sudo) pip install git+https://github.com/Phelimb/atlas

We recommend that you use virtualenv to install atlas - see instructions below:

Install atlas with virtualenv (recommended but optional)

Install virtualenv

Follow instruction at https://virtualenv.readthedocs.org/en/latest/installation.html

Create virtualenv

virtualenv venv

Activate the virtualenv

source venv/bin/activate

You can deactivate at anytime by typing deactivate in your terminal.

Install atlas

pip install git+https://github.com/Phelimb/atlas

Usage

usage: atlas [-h] [--version] {add,dump-probes,make-probes,genotype} ...

optional arguments:
  -h, --help            show this help message and exit
  --version             atlas version

[sub-commands]:
  {add,dump-probes,make-probes,genotype}
    add                 adds a set of variants to the atlas
    dump-probes         dump a panel of variant alleles
    make-probes         make probes from a list of variants
    genotype            genotype a sample using a probe set

Make probes

(venv)-bash-4.1$ ./mykatlas/atlas_main.py make-probes --help
usage: atlas make-probes [-h] [--db_name db_name] [-q] [-v VARIANT] [-f FILE]
                         [-g GENBANK] [-k KMER]
                         reference_filepath

positional arguments:
  reference_filepath    file path to reference

optional arguments:
  -h, --help            show this help message and exit
  --db_name db_name     db_name
  -q, --quiet           do not output warnings to stderr
  -v VARIANT, --variant VARIANT
                        Variant in DNA positions e.g. A1234T
  -f FILE, --file FILE  File containing variants as rows A1234T
  -g GENBANK, --genbank GENBANK
                        Genbank file containing genes as features
  -k KMER, --kmer KMER  kmer length

Examples

mykrobe make-probes -t example-data/staph-panel.txt -g BX571856.1.gb BX571856.1.fasta

mykrobe make-probes -t example-data/tb-walker-2015-panel.txt -g data/NC_000962.3.gb data/NC_000962.3.fasta

Citation

Please cite us if you use atlas in a publication

Bradley P, ... , Iqbal Z. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nature Communications 2015 Dec 21;6:10063
PMID: 26686880
DOI: 10.1038/ncomms10063

All analysis in this paper was done with release v0.1.3-beta.