prairiedog 0.2.0

Clone prairiedog and install lemongraph

git clone --recursive https://github.com/superphy/prairiedog.git
cd prairiedog/
python3 -m venv venv
. venv/bin/activate
cd lemongraph/
apt-get install libffi-dev zlib1g-dev python-dev python-cffi
python setup.py install

For creating a graph

. venv/bin/activate
pip install -r requirements.txt
pip install snakemake

For querying an existing graph

. venv/bin/activate
python setup.py install

Docker

docker run -v /abs-path-to/outputs/:/p/outputs/ -v /abs-path-to/samples/:/p/samples/ superphy/prairiedog dgraph

For creating a graph

. venv/bin/activate
snakemake -j 24 --config samples=samples/

For querying an existing graph

Via docker

# Without debug
docker run -v /home/kevin/pdg-test/outputs:/p/outputs/ -v /home/kevin/pdg-test/samples:/p/samples/ superphy/prairiedog:c6ff5c63779a73de02c9b3de0f4225b29564f285 query TCGAGCATTAT GCATAGGCAAC
# With debug
docker run -v /home/kevin/pdg-test/outputs:/p/outputs/ -v /home/kevin/pdg-test/samples:/p/samples/ superphy/prairiedog:c6ff5c63779a73de02c9b3de0f4225b29564f285 --debug query TCGAGCATTAT GCATAGGCAAC

or virtualenv

. venv/bin/activate
prairiedog ATACGACGCCA CGTCCGGACGT

You should get something like:

prairiedog GGGCGTTAAGT GGCAGGTTGAA
prairiedog[21238] INFO Looking for all strings between GGGCGTTAAGT and GGCAGGTTGAA ...
prairiedog[21238] INFO Found {'string': 'GGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAA', 'edge_type': 'SRR3295769.fasta', 'edge_value': '>SRR3295769.fasta|NODE_75_length_556_cov_349.837_ID_5290_pilon'}
prairiedog[21238] INFO Found {'string': 'GGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAA', 'edge_type': 'SRR3665189.fasta', 'edge_value': '>SRR3665189.fasta|NODE_60_length_523_cov_287.621_ID_4672'}

0.2.0 (2019-07-28)

• Pangenome graph creation via Dgraph

• Queries between kmers via Dgraph

0.1.2 (2019-06-21)

• Supports Pangenome graph creation

• Uses LemonGraph as backend

• Supports queries between any two kmers

0.1.1 (2019-05-25)

• Initial Snakefile for creating graphs

• Still need to add node_labels

0.1.0 (2019-05-08)

• First release on PyPI.