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TOC -->","maintainers":[{"name":"teselagen-admin","email":"devops@teselagen.com"},{"name":"tnrich","email":"tnrich@teselagen.com"},{"name":"colincwilson","email":"colin.wilson@teselagen.com"},{"name":"andres-teselagen","email":"aramirez@teselagen.com"},{"name":"tgreen-teselagen","email":"tgreen@teselagen.com"}],"readme":"# Bio Parsers\n\n<!-- TOC -->\n\n- [Bio Parsers](#bio-parsers)\n  - [About this Repo](#about-this-repo)\n  - [[CHANGELOG](CHANGELOG.md)](#changelogchangelogmd)\n  - [Exported Functions](#exported-functions)\n  - [Format Specification](#format-specification)\n  - [Usage](#usage)\n    - [install](#install)\n    - [jsonToGenbank (same interface as jsonToFasta)](#jsontogenbank-same-interface-as-jsontofasta)\n    - [anyToJson (same interface as genbankToJson, fastaToJson, xxxxToJson) (async required)](#anytojson-same-interface-as-genbanktojson-fastatojson-xxxxtojson-async-required)\n    - [Options (for anyToJson or xxxxToJson)](#options-for-anytojson-or-xxxxtojson)\n    - [ab1ToJson](#ab1tojson)\n    - [snapgeneToJson (.dna files)](#snapgenetojson-dna-files)\n    - [genbankToJson](#genbanktojson)\n  - [Updating this repo](#updating-this-repo)\n    - [Outside collaborators](#outside-collaborators)\n  - [Thanks/Collaborators](#thankscollaborators)\n\n<!-- /TOC -->\n\n## About this Repo\n\nThis repo contains a set of parsers to convert between datatypes through a generalized JSON format.\n\n## [CHANGELOG](CHANGELOG.md)\n\n## Exported Functions\n\nUse the following exports to convert to a generalized JSON format:\n\n```\nfastaToJson //handles fasta files (.fa, .fasta)\ngenbankToJson //handles genbank files (.gb, .gbk)\nab1ToJson //handles .ab1 sequencing read files\nsbolXmlToJson //handles .sbol files\ngeneiousXmlToJson //handles .genious files\njbeiXmlToJson //handles jbei .seq or .xml files\nsnapgeneToJson //handles snapgene (.dna) files\nanyToJson    //this handles any of the above file types based on file extension\n```\n\nUse the following exports to convert from a generalized JSON format back to a specific format:\n\n```\njsonToGenbank\njsonToFasta\njsonToBed\n```\n\n## Format Specification\n\nThe generalized JSON format looks like:\n\n```js\nconst generalizedJsonFormat = {\n  size: 25,\n  sequence: \"asaasdgasdgasdgasdgasgdasgdasdgasdgasgdagasdgasdfasdfdfasdfa\",\n  circular: true,\n  name: \"pBbS8c-RFP\",\n  description: \"\",\n  parts: [\n    {\n      name: \"part 1\",\n      type: \"CDS\", //optional for parts\n      id: \"092j92\", //Must be a unique id. If no id is provided, we'll autogenerate one for you\n      start: 10, //0-based inclusive index\n      end: 30, //0-based inclusive index\n      strand: 1,\n      notes: {}\n    }\n  ],\n  primers: [\n    {\n      name: \"primer 1\",\n      id: \"092j92\", //Must be a unique id. If no id is provided, we'll autogenerate one for you\n      start: 10, //0-based inclusive index\n      end: 30, //0-based inclusive index\n      strand: 1,\n      notes: {}\n    }\n  ],\n  features: [\n    {\n      name: \"anonymous feature\",\n      type: \"misc_feature\",\n      id: \"5590c1978979df000a4f02c7\", //Must be a unique id. If no id is provided, we'll autogenerate one for you\n      start: 1,\n      end: 3,\n      strand: 1,\n      notes: {}\n    },\n    {\n      name: \"coding region 1\",\n      type: \"CDS\",\n      id: \"5590c1d88979df000a4f02f5\",\n      start: 12,\n      end: 9,\n      strand: -1,\n      notes: {}\n    }\n  ],\n  //only if parsing in an ab1 file\n  chromatogramData: {\n    aTrace: [], //same as cTrace but for a\n    tTrace: [], //same as cTrace but for t\n    gTrace: [], //same as cTrace but for g\n    cTrace: [0, 0, 0, 1, 3, 5, 11, 24, 56, 68, 54, 30, 21, 3, 1, 4, 1, 0, 0, ...etc], //heights of the curve spaced 1 per x position (aka if the cTrace.length === 1000, then the max basePos can be is 1000)\n    basePos: [33, 46, 55, ...etc], //x position of the bases (can be unevenly spaced)\n    baseCalls: [\"A\", \"T\", ...etc],\n    qualNums: [] //or undefined if no qualNums are detected on the file\n  }\n};\n```\n\n## Usage\n\n### install\n\n`npm install -S @teselagen/bio-parsers`\n\nor\n\n`yarn add @teselagen/bio-parsers`\n\nor\n\nuse it from a script tag:\n\n```html\n<script src=\"https://unpkg.com/bio-parsers/umd/bio-parsers.js\"></script>\n<script>\n  async function main() {\n    var jsonOutput = await window.bioParsers.genbankToJson(\n      `LOCUS       kc2         108 bp    DNA     linear    01-NOV-2016\nCOMMENT             teselagen_unique_id: 581929a7bc6d3e00ac7394e8\nFEATURES             Location/Qualifiers\n     CDS             1..108\n                     /label=\"GFPuv\"\n     misc_feature    61..108\n                     /label=\"gly_ser_linker\"\n     bogus_dude      4..60\n                     /label=\"ccmN_sig_pep\"\n     misc_feature    4..60\n                     /label=\"ccmN_nterm_sig_pep\"\n                     /pragma=\"Teselagen_Part\"\n                     /preferred5PrimeOverhangs=\"\"\n                     /preferred3PrimeOverhangs=\"\"\nORIGIN      \n        1 atgaaggtct acggcaagga acagtttttg cggatgcgcc agagcatgtt ccccgatcgc\n       61 ggtggcagtg gtagcgggag ctcgggtggc tcaggctctg ggg\n//`\n    );\n    console.log(\"jsonOutput:\", jsonOutput);\n    var genbankString = window.bioParsers.jsonToGenbank(jsonOutput[0].parsedSequence);\n    console.log(genbankString);\n  }\n  main();\n</script>\n```\n\nsee the `./umd_demo.html` file for a full working example\n\n### jsonToGenbank (same interface as jsonToFasta)\n\n```js\n//To go from json to genbank:\nimport { jsonToGenbank } from \"bio-parsers\"\n//You can pass an optional options object as the second argument. Here are the defaults\nconst options = {\n  isProtein: false, //by default the sequence will be parsed and validated as type DNA (unless U's instead of T's are found). If isProtein=true the sequence will be parsed and validated as a PROTEIN type (seqData.isProtein === true)\n  guessIfProtein: false, //if true the parser will attempt to guess if the sequence is of type DNA or type PROTEIN (this will override the isProtein flag)\n  guessIfProteinOptions: {\n    threshold = 0.90, //percent of characters that must be DNA letters to be considered of type DNA\n    dnaLetters = ['G', 'A', 'T', 'C'] //customizable set of letters to use as DNA\n  },\n  inclusive1BasedStart: false //by default feature starts are parsed out as 0-based and inclusive\n  inclusive1BasedEnd: false //by default feature ends are parsed out as 0-based and inclusive\n  // Example:\n  // 0123456\n  // ATGAGAG\n  // --fff--  (the feature covers GAG)\n  // 0-based inclusive start:\n  // feature.start = 2\n  // 1-based inclusive start:\n  // feature.start = 3\n  // 0-based inclusive end:\n  // feature.end = 4\n  // 1-based inclusive end:\n  // feature.end = 5\n}\nconst genbankString = jsonToGenbank(generalizedJsonFormat, options)\n\n```\n\n### anyToJson (same interface as genbankToJson, fastaToJson, xxxxToJson) (async required)\n\n```js\nimport { anyToJson } from \"bio-parsers\";\n\n//note, anyToJson should be called using an await to allow for file parsing to occur (if a file is being passed)\nconst results = await anyToJson(\n  stringOrFile, //if ab1 files are being passed in you should pass files only, otherwise strings or files are fine as inputs\n  options //options.fileName (eg \"pBad.ab1\" or \"pCherry.fasta\") is important to pass here in order for the parser to!\n);\n\n//we always return an array of results because some files my contain multiple sequences\nresults[0].success; //either true or false\nresults[0].messages; //either an array of strings giving any warnings or errors generated during the parsing process\nresults[0].parsedSequence; //this will be the generalized json format as specified above :)\n//chromatogram data will be here (ab1 only):\nresults[0].parsedSequence.chromatogramData;\n```\n\n### Options (for anyToJson or xxxxToJson)\n\n```js\n//You can pass an optional options object as the third argument. Here are the defaults\nconst options = {\n  fileName: \"example.gb\", //the filename is used if none is found in the genbank\n  isProtein: false, //if you know that it is a protein string being parsed you can pass true here\n  parseFastaAsCircular: false; //by default fasta files are parsed as linear sequences. You can change this by setting parseFastaAsCircular=true\n  //genbankToJson options only\n  inclusive1BasedStart: false //by default feature starts are parsed out as 0-based and inclusive\n  inclusive1BasedEnd: false //by default feature ends are parsed out as 0-based and inclusive\n  acceptParts: true //by default features with a feature.notes.pragma[0] === \"Teselagen_Part\" are added to the sequenceData.parts array. Setting this to false will keep them as features instead\n  // fastaToJson options only\n  parseName: true //by default attempt to parse the name and description of sequence from the comment line. Setting this to false will keep the name unchanged with no description\n}\n```\n\n### ab1ToJson\n\n```js\nimport { ab1ToJson } from \"bio-parsers\";\nconst results = await ab1ToJson(\n  //this can be either a browser file  <input type=\"file\" id=\"input\" multiple onchange=\"ab1ToJson(this.files[0])\">\n  // or a node file ab1ToJson(fs.readFileSync(path.join(__dirname, './testData/ab1/example1.ab1')));\n  file,\n  options //options.fileName (eg \"pBad.ab1\" or \"pCherry.fasta\") is important to pass here in order for the parser to!\n);\n\n//we always return an array of results because some files my contain multiple sequences\nresults[0].success; //either true or false\nresults[0].messages; //either an array of strings giving any warnings or errors generated during the parsing process\nresults[0].parsedSequence; //this will be the generalized json format as specified above :)\n//chromatogram data will be here (ab1 only):\nresults[0].parsedSequence.chromatogramData;\n```\n\n### snapgeneToJson (.dna files)\n\n```js\nimport { snapgeneToJson } from \"bio-parsers\";\n//file can be either a browser file  <input type=\"file\" id=\"input\" multiple onchange=\"snapgeneToJson(this.files[0])\">\n// or a node file snapgeneToJson(fs.readFileSync(path.join(__dirname, './testData/ab1/example1.ab1')));\nconst results = await snapgeneToJson(file, options);\n```\n\n### genbankToJson\n\n```js\nimport { genbankToJson } from \"bio-parsers\";\n\nconst result = genbankToJson(string, options);\n\nconsole.info(result);\n// [\n//     {\n//         \"messages\": [\n//             \"Import Error: Illegal character(s) detected and removed from sequence. Allowed characters are: atgcyrswkmbvdhn\",\n//             \"Invalid feature end:  1384 detected for Homo sapiens and set to 1\",\n//         ],\n//         \"success\": true,\n//         \"parsedSequence\": {\n//             \"features\": [\n//                 {\n//                     \"notes\": {\n//                         \"organism\": [\n//                             \"Homo sapiens\"\n//                         ],\n//                         \"db_xref\": [\n//                             \"taxon:9606\"\n//                         ],\n//                         \"chromosome\": [\n//                             \"17\"\n//                         ],\n//                         \"map\": [\n//                             \"17q21\"\n//                         ]\n//                     },\n//                     \"type\": \"source\",\n//                     \"strand\": 1,\n//                     \"name\": \"Homo sapiens\",\n//                     \"start\": 0,\n//                     \"end\": 1\n//                 }\n//             ],\n//             \"name\": \"NP_003623\",\n//             \"sequence\": \"gagaggggggttatccccccttcgtcagtcgatcgtaacgtatcagcagcgcgcgagattttctggcgcagtcag\",\n//             \"circular\": true,\n//             \"extraLines\": [\n//                 \"DEFINITION  contactin-associated protein 1 precursor [Homo sapiens].\",\n//                 \"ACCESSION   NP_003623\",\n//                 \"VERSION     NP_003623.1  GI:4505463\",\n//                 \"DBSOURCE    REFSEQ: accession NM_003632.2\",\n//                 \"KEYWORDS    RefSeq.\"\n//             ],\n//             \"type\": \"DNA\",\n//             \"size\": 925\n//         }\n//     }\n// ]\n```\n\nYou can see more examples by looking at the tests.\n\n## Updating this repo\n\n### Outside collaborators\n\nfork and pull request please :)\n\n## Thanks/Collaborators\n\n- IsaacLuo - https://github.com/IsaacLuo/SnapGeneFileReader (from which the snapgene parser was adapted)\n- Joshua Nixon (original collaborator)\n- Thomas Rich (original collaborator)\n","readmeFilename":"README.md"}