augur.parse module

Parse delimited fields from FASTA sequence names into a TSV and FASTA file.

augur.parse.fix_dates(d, dayfirst=True)

attempt to parse a date string using pandas date parser. If ambiguous, the argument ‘dayfirst’ determines whether month or day is assumed to be the first field. Incomplete dates will be padded with XX. On failure to parse the date, the function will return the input.

augur.parse.prettify(x, trim=0, camelCase=False, etal=None, removeComma=False)

parse a fasta file and turn information in the header into a tsv or csv file.