subcommand - gisaid/ncbi reformatter

[ammaraziz]

A subcommand to handle metadata reformatting for gisaid or ncbi submission.

Possible names for subcommand:

metadata
meta-db
meta-formatter
reformat-meta

Example usage:

flukit metadata --meta input_meta.csv --format gisaid --output output_meta.tsv

flags:

-m, --meta
-f, --format
-o, --output

Formats:

• gisaid flu
• gisaid rsv (or 'new gisaid')
• ncbi rsv

Input is the output of fuzee - gisaid csv.

For gisaid use Rscript fuzee2gisaid.R script.