metadata_extraction: Metadata Extraction from NCBI/GISAID...

In vDiveR: Visualization of Viral Protein Sequence Diversity Dynamics

Metadata Extraction from NCBI/GISAID (EpiFlu/EpiCoV/EpiPox/EpiArbo) FASTA file

Description

This function retrieves metadata (ID, region, date) from the input FASTA file, with the source of, either NCBI (with default FASTA header) or GISAID (with default FASTA header). The function will return a dataframe that has three columns consisting ID, collected region and collected date. Records that do not have region or date information will be excluded from the output dataframe.

Usage

metadata_extraction(file_path, source)

Arguments

file_path	path of fasta file
source	the source of fasta file, either "NCBI" or "GISAID"

Value

A dataframe that has three columns consisting ID, collected region and collected date

Examples

filepath <- system.file('extdata','GISAID_EpiCoV.faa', package = 'vDiveR')
meta_gisaid <- metadata_extraction(filepath, 'GISAID')

vDiveR documentation built on April 4, 2025, 2:08 a.m.