biotech-js
v1.0.10
Published
Package developed at A&A Biotechnology for reading all kinds of biotechnology related files
Downloads
76
Maintainers
Readme
biotech-js
Package initially developed at and for A&A Biotechnology for reading all kinds of biotechnology related files.
Currently it supports fastq, fasta and genbank files.
Usage
Reading Fasta
file
import { FastaSequenceFile, ProcessingStatus } from "biotech-js";
const file = new FastaSequenceFile("path/to/file.fa");
await file.process();
expect(file.processingStatus).toBe(ProcessingStatus.SuccessFinished);
expect(file.sequences.length).toBe(12345);
expect(file.tookMs).toBeLessThan(1000);
await file.save();
// Default output path is "path/to/file_processed.fa"
// But you can customize it by passing a path to the save method
await file.save("path/to/file2.fa");
Reading Fastq
file
import { FastqSequenceFile, ProcessingStatus } from "biotech-js";
const file = new FastqSequenceFile("path/to/file1.fastq");
await file.process();
expect(file.processingStatus).toBe(ProcessingStatus.SuccessFinished);
expect(file.sequences.length).toBe(12345);
expect(file.tookMs).toBeLessThan(1000);
await file.save("path/to/file2.fastq");
Reading Genbank
file
import { GenbankSequencesFile, ProcessingStatus } from "biotech-js";
const file = new GenbankSequencesFile("path/to/file1.gb");
await file.process();
expect(file.processingStatus).toBe(ProcessingStatus.SuccessFinished);
expect(file.sequences.length).toBe(12345);
expect(file.tookMs).toBeLessThan(1000);
await file.save("path/to/file2.gb");
Detecting file extension
import { FileExtensionHandler } from "biotech-js";
const path = "path/to/file.fa";
const pathExtension = path.split(".").pop();
const extension = FileExtensionHandler.fileExtensionToEnum(pathExtension);
console.log(extension);
// Output: Fasta
Deployment
When deploying the library to npm run:
yarn b