metadata_extraction {vDiveR} | R Documentation |
Metadata Extraction from NCBI/GISAID EpiCoV 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')
[Package vDiveR version 2.0.0 Index]