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.

More info about BLAST

Getting Started

Install the module with: npm install biojs-io-blast

var blast = require('biojs-io-blast');
blast.read("http://files.biojs.net/blast/examples/syne1.xml", function(data){
    console.log("blast object", data);
}); 

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Documentation

BLAST: short recap (with the output format)

.read(url)

Parameter: URL of a BLAST output (in xml) Type: String Example: http://files.biojs.net/blast/examples/syne1.xml

Parameter: Callback or promise Type: function

Downloads the XML BLAST file and parses it to JSON.

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.

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: String Example: <BlastOutput><BlastOutput_program>blastp</BlastOutput_program></BlastOutput>

Parses the BLAST XML output to JSON.

blast.parse('<BlastOutput><BlastOutput_program>blastp</BlastOutput_program></BlastOutput>'); 

CLI version

Install it globally npm install -g biojs-io-blast and then you can pipe directly into the parser.

cat <blast-file.xml> | biojs-blast

Output

• there can be multiple iterations
• there can be multiple per hits per iteration
• there can be multiple HSPS per hit

Full example

Official BLAST XML spec

{
    "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"
            }
        }
    ]
}

Contributing

Please submit all issues and pull requests to the greenify/biojs-io-blast repository.

Support

If you have any problem or suggestion please open an issue here.

License

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.