Parse sequence files (GenBank, FASTA, SnapGene, SBOL) and accession IDs (NCBI, iGEM) to a common format
npm install seqparseParse sequence files (GenBank, FASTA, JBEI, SnapGene, SBOL) or accession IDs (NCBI, iGEM) to a simple, common format:
``ts
interface Seq {
name: string;
type: "dna" | "rna" | "aa" | "unknown";
seq: string;
annotations: Annotation[];
}
interface Annotation {
name: string;
start: number;
end: number;
direction?: number;
color?: string;
type?: string;
}
`
`bash`
npm i seqparse
To install the CLI globally:
`bash`
npm i -g seqparse
`ts
import seqparse from "seqparse";
const { name, type, seq, annotations } = await seqparse(file);
`
Example outputs are truncated for clarity.
`bashparse files
$ seqparse pBbE0c-RFP.gb
{
"name": "pBbE0c-RFP",
"type": "dna",
"seq": "cagctagctcagtcctaggtactgtgctagctacta...",
"annotations": [
{
"name": "colE1 origin",
"start": 1234,
"end": 1917,
"direction": -1,
"type": "rep_origin"
},
...