npm install bio.ioCollection of JavaScript module to parse biological formats.
* Remember that you need CORS to download files from other servers on the web
FASTA
-----
``
var Fasta = require('biojs-io-fasta');
#### read(url)
Parses an url an calls your parse method with the returned body.
`
Fasta.read("https://raw.githubusercontent.com/biojs-io/biojs-io-fasta/master/test/foo.fasta", function(err, model) {
// model is the parsed url
});
If callback is undefined, returns a promise.
`
var p = Fasta.read("https://raw.githubusercontent.com/biojs-io/biojs-io-fasta/master/test/foo.fasta");
// ...
p.then(function(model) {
// model is the parsed url
}, function(err){
console.error("err happened during downloading", err);
});
`
var seqs = Fasta.parse(str);
`
var text = Fasta.export(seqs);
Thanks to @sillitoe you can provide a custom parser
if your FASTA header is formatted "in weird and wonderful ways".
`
var customGetMeta = function(header) {
return {
id: "id",
name: "name",
// optional
details: {
foo: "bar"
},
// optional
ids: {
customId: "bar"
}
};
}
var altFasta = Fasta.extend(customGetMeta);
Take a look at tests
for a better example of such a parser;
Sequence object
---------------
`
{
seq: "ABC",
name: "awesome seq",
id: "unique id"
}
Clustal
-------
#### read(url)
Parses an url an calls your parse method with the returned body.
`
Clustal.read("https://raw.githubusercontent.com/greenify/biojs-io-clustal/blob/master/test/p53.clustalo.clustal", function(err, model) {
// model is the parsed url
});
If callback is undefined, returns a promise.
`
Clustal.read("https://raw.githubusercontent.com/greenify/biojs-io-clustal/blob/master/test/p53.clustalo.clustal").then(function(model) {
// model is the parsed url
}, function(err){
console.error("err happened during downloading", err);
});
function is your async callback.
`
var seqs = Clustal.parse(str);
Sequence object
---------------
`
this.seq
this.name
this.id
st.getMeta("sp|abc|def") // {name: "def", ids: {sp: "abc"}}
`
st.contains("ABC", 2) // false
st.contains("ABC","C") // true
`
st.splitNChars("ABC", 2) // ["AB", "C"]
GFF (General feature format)
----------------------------
> A GFF (general feature format) parser
`
Short description about the formats.
* GFF 3
* Jalview feature format
javascript
var gff = require('biojs-io-gff');
`Documentation
####
Callback with
or Promise`javascript
var p = gff.read("https://cdn.rawgit.com/greenify/biojs-io-gff/master/test/import.gff3");
// ..
p.then(function(seqs){
// handle the model
}, function(err){
console.warn(err);
});
`####
(alias: parse)Parameter:
GFF file (as string)
Type: String
Example: Returns a dictionary of all sequences. Each sequences is an array of its features.
javascript
gff.parseSeqs('SEQ1 EMBL atg 103 105 . + 0');
`__Result__
{ "seqs":
{ "SEQ1":
[ { seqname: 'SEQ1',
source: 'EMBL',
feature: 'atg',
start: 103,
end: 105,
strand: '+',
frame: 0,
attributes: {} } ]
},
"config": {
type: "gff3"
}
}
####
Parameter:
Type:
Example: The 'parse' method converts a GFF into its JSON representation.
How to use this method
javascript
gff.parseLines('SEQ1 EMBL atg 103 105 . + 0');
`__Result__
{ "features":
[{ seqname: 'SEQ1',
source: 'EMBL',
feature: 'atg',
start: 103,
end: 105,
strand: '+',
frame: 0,
attributes: {} } ],
"config": {
type: "gff3"
}
}
#### Return the textual GFF representation for the given lines
####
(alias: export)Return the textual GFF representation for the given seqs
####
.parseLine(line)Parameter:
Type:
Example: The 'parseLine' method converts a GFF line into its JSON representation.
javascript
gff.parseLine('SEQ1 EMBL atg 103 105 . + 0');
`Gotchas
* undefined properties (dots) are removed (checking for undefined is native)
Parser API
==========
It expects that you provide at least a method
(see below for more details).Provided methods
---------------
####
read(url)Parses an url an calls your
method with the returned body.`
parser.read("http://your-url", function(err, model) {
// model is the parsed url
});
If callback is undefined, returns a promise.`
parser.read("http://your-url").then(function(model) {
// model is the parsed url
}, function(err){
console.error("err happened during downloading", err);
});
Expected methods
----------------
Your parser should have the following methods:
*
: Takes in an entire file as string and returns the JSON representationOptional:
*
write: Takes the JSON representation of a file and writes it in the custom formatIf the file is line-by-line, one should create a
new instance of the parser:*
parseLine: parses another line
* result: returns the current, resulting object of the parsing process.How to extend
-------------
$3
`
var parser = function(){
this.parse = function(data){
return data;
};
Parser.mixin(this);
};
$3
var throughParserAlt = {
parse: function(data) {
return data;
}
};
Matrix
------
> Parse 2D matrices (e.g. PAM)
$3
Parses an url an calls your
method with the returned body.`
MParser.read("https://cdn.rawgit.com/greenify/biojs-io-matrix/master/test/data/pam_250", function(err, model) {
// model is the parsed url
});
If callback is undefined,
returns a promise.`
var p = MParser.read("https://cdn.rawgit.com/greenify/biojs-io-matrix/master/test/data/pam_250");
// ...
p.then(function(model) {
// model is the parsed url
}, function(err){
console.error("err happened during downloading", err);
});
$3
var matrix = MParser.parse("A 1\nB 1 2");
> { A: { A: 1, B: 1 },
B: { A: 1, B: 2 } }
$3
var mParser = new MParser();
mParser.parseLine("A 1");
mParser.parseLine("B 2 3");
var matrix = mParser.buildMatrix();
$3
var matrix = MParser("A 1\nB 1 2");
var out = mParser.export(matrix);
> 'A\t1\nB\t1\t2'
Or you can use objects
var matrix = new MParser("A 1\nB 1 2");
matrix.buildMatrix(); \\ returns the 2D array
var out = matrix.export();
> 'A\t1\nB\t1\t2'
BLAST
-----
> BLAST parser
It parses the XML output of BLAST. You can activate the XML output by adding the
flag to your BLAST program.Getting Started
Install the module with: npm install biojs-io-blastjavascript
var blast = require('biojs-io-blast');
blast.read("http://files.biojs.net/blast/examples/syne1.xml", function(data){
console.log("blast object", data);
});
`Documentation
BLAST: short recap (with the output format)
####
Parameter:
Type:
Example: Parameter:
or promise
Type: functionDownloads 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.
####
Parameter:
Type:
Example: Parses the BLAST XML output to JSON.
javascript
blast.parse('blastp
`CLI version
Install it globally
and then you can pipe directly into the parser.`
cat | biojs-blast
Output
* there can be multiple iterations
* there can be multiple per hits per iteration
* there can be multiple HSPS per hit
$3
{
"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"
}
}
]
}
Newick Parser
----------
Just call method
for parsing a newick string into JSON.`javascript
Biojs.io.newick.parse_newick('((A,B),C)');
`Call the method
for parsing an extended newick formats into JSON.`javascript
Biojs.io.newick.parse_nhx('((A,B),C)');
`Newick format:
sh
(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F
`Converted to JSON:
javascript
{name : "F",
children: [
{name: "A", branch_length: 0.1},
{name: "B", branch_length: 0.2},
{
name: "E",
length: 0.5,
children: [
{name: "C", branch_length: 0.3},
{name: "D", branch_length: 0.4}
]
}
]
}
``