@lipme/ts-biofiledetector v0.0.3

TS-BIOFILEDETECTOR

Overview

A set of function to predict file formats

Formats included:

• Fasta (proteic/nucleic)
• GFF3 (annotation/alignment)
• BED
• VCF
• BAM (to improve)

Installation

npm i @lipme/ts-biofiledetector

Usage

import { getFileFormat } from "@lipme/ts-biofiledetector";

Output

• Fasta

{
  format: "fasta",
  valid: true|false,
  metadata: {
    type: "dna|protein",
    seqids: ['list','of','seqids']
    error?: { 'errorType' : ['list', 'of', 'erroneous', 'lines']}
  }
}

• GFF3

{
    format: "gff3",
    valid: true|false,
    metadata: {
    type: "annotation|alignment",
    seqids: ['list','of','seqids'],
    features: ['list', 'of', 'features'],
    attributes: ['list', 'of', 'attributes'],
    error?: { 'errorType' : ['list', 'of', 'erroneous', 'lines']}
  }
}

• BED

{
  format: "bed",
  valid: true|false,
  metadata: {
    type: "bed3|bed4|bed6|bed9|bed12",
    seqids: ['list','of','seqids'],
    columns: "numberOfColumns",
    withBrowser: true|false, //browser line found
    withTrack: true|false, //track line found
    error?: { 'errorType' : ['list', 'of', 'erroneous', 'lines']}
  }
}

• VCF

{
  format: "vcf",
  valid: true|false,
  metadata: {
    type: "VCFversion",
    seqids: ['list','of','seqids'],
    samples: ['list','of','samples'],
    error?: { 'errorType' : ['list', 'of', 'erroneous', 'lines']}
    }
}

License

This project is licensed under the Apache License 2.0. See the LICENSE file for details.

Contact

For questions or feedback, please open an issue or contact us at sebastien.carrere@inrae.fr