npm install biojs-io-blast
> BLAST parser
It parses the XML output of BLAST. You can activate the XML output by adding the -outfmt 5 flag to your BLAST program.
npm install biojs-io-blast``javascript`
var blast = require('biojs-io-blast');
blast.read("http://files.biojs.net/blast/examples/syne1.xml", function(data){
console.log("blast object", data);
});
BLAST: short recap (with the output format)
#### .read(url)
Parameter: URL of a BLAST output (in xml)
Type:
Example:
Parameter: Callback or promisefunction
Type:
Downloads the XML BLAST file and parses it to JSON.
`javascript`
blast.read('http://files.biojs.net/blast/examples/syne1.xml', function(err, data){
console.log("blast object", data);
});
If you don't specify a callback, it will return a promise.
`javascript`
var p = blast.read("https://raw.githubusercontent.com/greenify/biojs-io-blast/master/test/dummy/single.xml");
p.then(function(model) {
// model is the parsed url
}, function(err){
console.error("err happened during downloading", err);
});
As downloading the file is asynchronous, it will call your callback with the
resulting data object.
#### .parse(str)
Parameter: XML Output of BLAST
Type:
Example:
Parses the BLAST XML output to JSON.
`javascript`
blast.parse('
Install it globally npm install -g biojs-io-blast and then you can pipe directly into the parser.
`
cat Output
* there can be multiple iterations
* there can be multiple per hits per iteration
* there can be multiple HSPS per hit
`
{
"program": "blastp",
"version": "BLASTP 2.2.29+",
"reference": "Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), \"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs\", Nucleic Acids Res. 25:3389-3402.",
"db": "/home/xsebi/tmp/blast/swiss",
"query-ID": "Query_1",
"query-def": "sp|Q8NF91|SYNE1_HUMAN Nesprin-1 OS=Homo sapiens GN=SYNE1 PE=1 SV=4",
"query-len": "8797",
"param": {
"matrix": "BLOSUM62",
"expect": "10",
"gap-open": "11",
"gap-extend": "1",
"filter": "F"
},
"iterations": [
{
"iter-num": "1",
"query-ID": "Query_1",
"query-def": "sp|Q8NF91|SYNE1_HUMAN Nesprin-1 OS=Homo sapiens GN=SYNE1 PE=1 SV=4",
"query-len": "8797",
"hits": [
{
"num": "1",
"id": "gnl|BL_ORD_ID|140988",
"def": "gi|425906075|sp|Q8NF91.4|SYNE1_HUMAN RecName: Full=Nesprin-1; AltName: Full=Enaptin; AltName: Full=Myocyte nuclear envelope protein 1; Short=Myne-1; AltName: Full=Nuclear envelope spectrin repeat protein 1; AltName: Full=Synaptic nuclear envelope protein 1; Short=Syne-1 [Homo sapiens]",
"accession": "140988",
"len": "8797",
"hsps": [
{
"num": "1",
"bit-score": "17954.1",
"score": "46598",
"evalue": "0",
"query-from": "1",
"query-to": "8797",
"hit-from": "1",
"hit-to": "8797",
"query-frame": "0",
"hit-frame": "0",
"identity": "8797",
"positive": "8797",
"gaps": "0",
"align-len": "8797",
"qseq": "MATSRGASRCPR...",
"hseq": "MATSRGASRCPR...",
"midline": "MATSRGASRCPR..."
}
]
"stat": {
"db-num": "459767",
"db-len": "171814008",
"hsp-len": "143",
"eff-space": "917906647858",
"kappa": "0.041",
"lambda": "0.267",
"entropy": "0.14"
}
}
]
}
Please submit all issues and pull requests to the greenify/biojs-io-blast repository.
This software is licensed under the Apache 2 license, quoted below.
Copyright (c) 2014, greenify
Licensed under the Apache License, Version 2.0 (the "License"); you may not
use this file except in compliance with the License. You may obtain a copy of
the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
License for the specific language governing permissions and limitations under
the License.