@tomek7667/tmk-biotech

Package tmk-biotech

Used for reading fasta and fastq files and structuring as valid javascript objects. The package provides also some useful utility functions like complementarify used for getting complementary sequence, or sanitizeGenome for sanitizing user input.

Example usage:

const {
	loadFastFile,
	loadFastArchive,
	complementarify,
	sanitizeGenome,
	makeSureDirectory,
	getAppDataPath,
	supportedFileTypes,
} = require('@tomek7667/tmk-biotech');

// Loading genomes from a file (with their qualities), a custom error callback can be specified in case of invalid format of a file.
const dataObject = loadFastFile("path/to/file.fastq", () => { console.log("Custom error when invalid format"); }) // Or .fa or .fasta
// OUT: 
// {
// 	"readsNames": ["Read 1", "Read 2"],
// 	"reads": ["GAATA", "TGTGG"],
// 	"readsQualities": [[0, 0, 0, 0, 0], [1, 2, 5, 2, 0]],
// 	"type": "fastq"
// }

// Loading genomes from a '.gz' archive (with one file currently tested). A custom error callback can be specified in case of invalid format of a file.
const dataObject = await loadFastArchive("path/to/file.fastq.gz", "Test app", () => { console.log("Custom error when invalid format"); }) // Or .fa.gz or .fasta.gz
// OUT:
// {
// 	"readsNames": ["Read 1", "Read 2"],
// 	"reads": ["GAATA", "TGTGG"],
// 	"readsQualities": [[0, 0, 0, 0, 0], [1, 2, 5, 2, 0]],
// 	"type": "fastq"
// }

// Returning complementary sequence to the input one
const complementarySequence = complementarify("GAATACCACA")
// OUT: TGTGGTATTC

// Sanitizes user input
const sanitizedGenome = sanitizeGenome("gA tcca ACa \n")
// OUT: GATCCAACA

// Recursively ensuring a directory exists
makeSureDirectory("/path/to/dir")

// Getting absolute path to the directory of the current project/app
const pathToFileStoring = getAppDataPath("Test app")

// Getting supported file extensions
console.log(supportedFileTypes)
// OUT: ["fa", "fasta", "fastq", "fastq.gz", fasta.gz", "fa.gz"]

// Generate all GATC sequences 
const gatcSequences = iupacTOgatc("TTTRT");

console.log(gatcSequences);
// OUT: [ 'TTTAT', 'TTTGT' ]