thomasstjerne/blast-ws

blast-ws

A thin rest service on top af blast.

Requirements

• Node version v8.9.4 installed.
• blast installed, and a blast database created for querying

Install

Download a reference dataset: https://unite.ut.ee/repository.php - choose the "General FASTA release"

Make a blast database:

makeblastdb -in sh_general_release_dynamic_01.12.2017.fasta -title unite -parse_seqids -dbtype nucl

Clone this repository:

git clone https://github.com/thomasstjerne/blast-ws.git

cd in to the directory:

cd blast-ws

install dependencies:

npm install

Run the service

node app.js

Usage

POST http://localhost:9000/blast

The body of your request should be a JSON object:

{
  "marker": "ITS", 
  "sequence": "TTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTGAAATAAACCT......."
 }

Example

curl --header "Content-Type: application/json" \
  --request POST \
  --data '{"sequence" : "TTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTGAAATAAACCTGATGAGTTGTTGCTGGCTCTCTAGGGAGCATGTGCACACTTGTCATCTTTGTATCTTCACCTGTGCACCTTTTGTAGACCTTGGGTATCTATCTGATTGCTTTAGCACTCAGGATTGAGGATTGACTTCTTGTCTCTTCTTACATTTCCAGGTCTATGTTTCTTAATATACCCTAATGTATGTTTATAGAATGTAATTAATGGGCCTTTGTGCCTATAAATCTATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCATTAATATATCAACCTCTTTGGTTGGATGTGGGGGTTTGCTGGCCACTTGAGGTCAGCTCCTCTTAAATGCATTAGCGGACAACATTTTGCTAAACGTTCATTGGTGTGATAATTATCTACGCTCTTGACGTGAAGCAGGTTCAGCTTCTAACAGTCCATTGACTTGGATAAATTTTTTTCTATCAATGTGACCTCAAATCAGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACTAACAAGGATTCCCCTAGTAACTGCGAGTGAAGCGGGAAAAGCTCAAATTTAAAATCTGGCAGTCTTTGGCTGTCCGAGTTGTAATCTAGAGAAGCATTATCCGCGCTG",
	"marker": "ITS"
}' \
  http://localhost:9000/blast | node <<< "var o = $(cat); console.log(JSON.stringify(o, null, 4));"

HBase cache

create 'blast_cache', {NAME=>'ref', VERSIONS => 1, COMPRESSION => 'SNAPPY', DATA_BLOCK_ENCODING => 'FAST_DIFF', BLOOMFILTER => 'NONE'}

hosts: c4master1-vh.gbif.org, c4master2-vh.gbif.org, c4master2-vh.gbif.org
port: 9090

ssh [email protected]
> hbase shell
hbase> count 'blast_cache'
hbase> scan 'blast_cache'