pombredanne / atlas-1 Goto Github PK

git clone --recursive [email protected]:Phelimb/atlas.git    
python setup.py install

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

virtualenv venv

source venv/bin/activate

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

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

(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

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