ctb / 2017-sourmash-lca Goto Github PK

sudo apt-get update && sudo apt-get -y install unzip
wget https://downloads.rclone.org/rclone-v1.38-linux-amd64.zip
cd rclone-*-linux-amd64
sudo cp rclone /usr/bin/
sudo chown root:root /usr/bin/rclone
sudo chmod 755 /usr/bin/rclone

rclone sync remote:kraken_db .

sudo apt-get -y update && \
sudo apt-get install -y python3.5-dev python3.5-venv make \
    libc6-dev g++ zlib1g-dev

python3.5 -m venv ~/sourmash20171007
. ~/sourmash20171007/bin/activate
pip install -U pip
pip install -U Cython
pip install -U jupyter jupyter_client ipython pandas matplotlib scipy scikit-learn khmer

pip install -U https://github.com/dib-lab/sourmash/archive/master.zip

git clone https://github.com/ctb/2017-sourmash-lca.git

cd ~/sourmash_sigs
for infile in library/*/*/*.fna
do
  sourmash compute -k 21,31,51 --output ${infile}.sig --scaled 10000 --name-from-first ${infile}
done

mkdir refseq_lca
cd refseq_lca
mkdir genbank
cd genbank
curl -O -L ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar xzf taxdump.tar.gz nodes.dmp names.dmp
cd ..

curl -O -L https://github.com/dib-lab/2017-ncbi-taxdump/raw/master/genbank-genomes-accession%2Blineage-20170529.csv.gz

~/2017-sourmash-lca/extract.py sbt.lca genbank*.csv.gz genbank/nodes.dmp ~/sourmash_sigs/library/*/*/*.sig --lca-json=sbt.lca.json

scp -i ~/pat/to/key ~/Desktop/mircea/SRR606249.pe.qc.fq.gz.abundtrim.gz [email protected]:~/

sourmash compute -k 21,31,51 --scaled 10000 -o SRR606249.pe.qc.fq.gz.abundtrim.sig SRR606249.pe.qc.fq.gz.abundtrim.gz

~/2017-sourmash-lca/classify.py -k 31 ~/refseq_lca/sbt.lca.json ~/SRR606249.pe.qc.fq.gz.abundtrim.sig

loading taxonomic nodes from: /home/ubuntu/refseq_lca/genbank/nodes.dmp
loading taxonomic names from: /home/ubuntu/refseq_lca/genbank/names.dmp
loading k-mer DB from: /home/ubuntu/refseq_lca/sbt.lca
loading signatures from 1 signature files
loaded 1 signatures total at k=31
downsampling to scaled value: 10000
found LCA classifications for 0 of 6228 hashes
cannot find taxid 0; quitting.
percent	below	at node	code	taxid	name
100.0	6228	6228	-	0	-
100.0	6228	6228	U	0	not classified

mkdir ~/genbank_lca
cd genbank_lca

curl -L https://osf.io/zfmbd/download?version=1 -o genbank-lca-2017.08.26.tar.gz
tar xzf genbank-lca-2017.08.26.tar.gz

~/2017-sourmash-lca/classify.py ~/genbank_lca/genbank.lca.json SRR606249.pe.qc.fq.gz.abundtrim.sig