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library of parsers for interconverting between genbank, fasta, and (eventually) sbol through Teselagen's intermediary json format","maintainers":[{"email":"devops@teselagen.com","name":"teselagen-admin"},{"email":"colin.wilson@teselagen.com","name":"colincwilson"},{"email":"aramirez@teselagen.com","name":"andres-teselagen"},{"email":"tgreen@teselagen.com","name":"tgreen-teselagen"},{"email":"trich1230@gmail.com","name":"tnrich"}],"readme":"# Bio Parsers\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  - [Editing This Repo](#editing-this-repo)\n    - [All collaborators:](#all-collaborators)\n  - [Debug](#debug)\n  - [Updating this repo](#updating-this-repo)\n    - [Teselagen collaborators](#teselagen-collaborators)\n    - [Outside collaborators](#outside-collaborators)\n  - [Thanks/Collaborators](#thankscollaborators)\n\n<!-- /TOC -->\n## About this Repo\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\nUse the following exports to convert to a generalized JSON format:\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```\njsonToGenbank\njsonToFasta\njsonToBed\n```\n\n\n## Format Specification\nThe generalized JSON format looks like:\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\n## Usage\n### install\n`npm install -S bio-parsers` \n\nor \n\n`yarn add bio-parsers`\n\nor \n\nuse it from a script tag: \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\n\n\nsee the `./umd_demo.html` file for a full working example\n\n### jsonToGenbank (same interface as jsonToFasta)\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### 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```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```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```\n\nYou can see more examples by looking at the tests.\n\n\n\n## Editing This Repo\n### All collaborators:\nEdit/create a new file and update/add any relevant tests.\nMake sure they pass by running `yarn test`\n\n## Debug\n```\nyarn test-debug\n```\n\n## Updating this repo\n### Teselagen collaborators\nCommit and push all changes\nSign into npm using the teselagen npm account (npm whoami)\n\n```\nnpm version patch|minor|major\nnpm publish\n```\n\n### Outside collaborators\nfork and pull request please :)\n\n\n## Thanks/Collaborators\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"}