# bio.io > Biological parsers Latest version **1.0.6** (published 2016-06-03) · MIT license · 0 weekly downloads ## Install ```sh npm install bio.io pnpm add bio.io yarn add bio.io bun add bio.io ``` ## Health **Score 15/100 (F)** — status: abandoned. Positive: no vulnerabilities. Warnings: low downloads; no types; no esm support. Negative: abandoned; low maintenance score. ## Facts | | | |---|---| | Version | 1.0.6 | | Published | 2016-06-03 | | First published | 2016-06-03 | | Weekly downloads | 0 | | License | MIT | | TypeScript types | none | | Module format | CommonJS | | Dependencies | 4 | | Known vulnerabilities | 0 (+1 in 1 direct dependencies) | | Install scripts | no | | Author | Sebastian Wilzbach | | Maintainers | greenify | | Keywords | biological, format, parser | ## Links - npm: https://www.npmjs.com/package/bio.io - npm.io page: https://npm.io/package/bio.io ## Dependencies (4) - [vow](https://npm.io/package/vow.md) ^0.4.12 - [xhr](https://npm.io/package/xhr.md) ^2.2.0 - [xmldoc](https://npm.io/package/xmldoc.md) ^0.5.1 - [request](https://npm.io/package/request.md) ^2.72.0 ## Alternatives - [babylon](https://npm.io/package/babylon.md) — 5.1M weekly downloads - [csscolorparser](https://npm.io/package/csscolorparser.md) — 3.7M weekly downloads - [expr-eval-fork](https://npm.io/package/expr-eval-fork.md) — 1.5M weekly downloads - [@leeoniya/ufuzzy](https://npm.io/package/@leeoniya/ufuzzy.md) — 247.7K weekly downloads - [xml-parser](https://npm.io/package/xml-parser.md) — 78.4K weekly downloads ## Recent versions - 1.0.6 (latest) — 2016-06-03 - 1.0.5 — 2016-06-03 - 1.0.4 — 2016-06-03 - 1.0.3 — 2016-06-03 - 1.0.2 — 2016-06-03 - 1.0.0 — 2016-06-03 ## README # bio.io Collection of JavaScript module to parse biological formats. [![NPM version](http://img.shields.io/npm/v/bio.io.svg)](https://www.npmjs.org/package/bio.io) [![Build Status](https://travis-ci.org/wilzbach/bio.io.svg?branch=master)](https://travis-ci.org/wilzbach/bio.io) ### Gotchas * Remember that you need [CORS](http://en.wikipedia.org/wiki/Cross-origin_resource_sharing) 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, `read` 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); }); ``` ### `parse(str)` ``` var seqs = Fasta.parse(str); ``` ### `export(model)` ``` var text = Fasta.export(seqs); ``` ### `extend(customParser)` Thanks to [@sillitoe](https://github.com/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](https://github.com/biojs-io/biojs-io-fasta/blob/master/test/fasta.js#L56) 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, `read` 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. ### `parse(str)` ``` var seqs = Clustal.parse(str); ``` Sequence object --------------- ``` this.seq this.name this.id ``` ## Seq.tools ### st.getMeta(label) `` st.getMeta("sp|abc|def") // {name: "def", ids: {sp: "abc"}} `` ### st.contains(text,search) ``` st.contains("ABC", 2) // false st.contains("ABC","C") // true ``` ### st.splitNChars(text,n) ``` st.splitNChars("ABC", 2) // ["AB", "C"] ``` GFF (General feature format) ---------------------------- > A GFF (general feature format) parser [Official Spec](https://www.sanger.ac.uk/resources/software/gff/spec.html) ``` [attributes] [comments] ``` Short [description about the formats](https://github.com/greenify/biojs-vis-msa/wiki/Annotation-Features). ## Supported formats * [GFF 3](http://www.sequenceontology.org/gff3.shtml) * [Jalview feature format](http://www.jalview.org/help/html/features/featuresFormat.html) ## Getting Started Install the module with: `npm install biojs-io-gff` ```javascript var gff = require('biojs-io-gff'); ``` ## Documentation #### `.read(file, cb)` Callback with `parseSeqs` 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); }); ``` #### `.parseSeqs(str)` (alias: `parse`) **Parameter**: `GFF file` (as string) **Type**: `String` **Example**: `SEQ1 EMBL atg 103 105 . + 0` 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" } } ``` #### `.parseLines(str)` **Parameter**: `GFF file` **Type**: `String` **Example**: `SEQ1 EMBL atg 103 105 . + 0` 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" } } ``` #### `.exportLines(lines)` Return the textual GFF representation for the given lines #### `.exportSeqs(seqs)` (alias: `export`) Return the textual GFF representation for the given seqs #### `.parseLine(line)` **Parameter**: `GFF line` **Type**: `String` **Example**: `SEQ1 EMBL atg 103 105 . + 0` 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 `parse` (see below for more details). Provided methods --------------- #### `read(url)` Parses an url an calls your `parse` method with the returned body. ``` parser.read("http://your-url", function(err, model) { // model is the parsed url }); ``` If callback is undefined, `read` 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: * `parse`: Takes in an entire file as string and returns the JSON representation Optional: * `write`: Takes the JSON representation of a file and writes it in the custom format If 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 ------------- ### With functions ``` var parser = function(){ this.parse = function(data){ return data; }; Parser.mixin(this); }; ``` ### With objects ``` var throughParserAlt = { parse: function(data) { return data; } }; ``` Matrix ------ > Parse 2D matrices (e.g. PAM) ### `read(url)` Parses an url an calls your `parse` 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, `read` 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); }); ``` ### Read a entire file ``` var matrix = MParser.parse("A 1\nB 1 2"); > { A: { A: 1, B: 1 }, B: { A: 1, B: 2 } } ``` ### Line by line ``` var mParser = new MParser(); mParser.parseLine("A 1"); mParser.parseLine("B 2 3"); var matrix = mParser.buildMatrix(); ``` ### Save a matrix ``` 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 `-outfmt 5` flag to your BLAST program. [More info about BLAST](http://www.ncbi.nlm.nih.gov/books/NBK153387/) ## Getting Started Install the module with: `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); }); ``` [Play on JSBin](http://jsbin.com/cidoga/1/edit?js,console) ## Documentation [BLAST: short recap (with the output format)](https://docs.google.com/presentation/d/1OtYi-ihHapeHRq_PTc3fi7grnbHoXMbJBJI4Yq1kKGo/present?usp=sharing&slide=id.p) #### `.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. ```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**: `String` **Example**: `blastp` Parses the BLAST XML output to JSON. ```javascript blast.parse('blastp'); ``` ## CLI version Install it globally `npm install -g biojs-io-blast` 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 ### Full example ![entity diagram](http://i.imgur.com/icB9EuG.png) [Official BLAST XML spec](http://tinyurl.com/ncbi-blast-xml) ``` { "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 `parse_newickk(string)` for parsing a newick string into JSON. ```javascript Biojs.io.newick.parse_newick('((A,B),C)'); ``` Call the method `parse_nhx(string)` for parsing an extended newick formats into JSON. ```javascript Biojs.io.newick.parse_nhx('((A,B),C)'); ``` [Example tree](http://en.wikipedia.org/wiki/Newick_format): 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} ] } ] } ``` --- _Source: https://npm.io/package/bio.io · Machine-readable twin of the npm.io package page. Health data is recomputed on every publish._