adds an ordinal date field based on a timestamp to a q2 metadata file

convert_timestamp_to_ordinal_date.py

#! /usr/bin/env python3
from qiime2 import Metadata
from dateutil.parser import parse
from dateutil.relativedelta import relativedelta

m = Metadata.load("metadata-with-age.tsv")
m_df = m.to_dataframe()

m_df["ordinal-timestamp"] = 0

for sample_id in m_df.index:
    parsed_date = parse(m_df.loc[sample_id, "collection_timestamp"])
    parsed_date_ordinalstring = parsed_date.isoformat()[:10].replace("-", "")
    m_df.loc[sample_id, "ordinal-timestamp"] = parsed_date_ordinalstring

Metadata(m_df).save("metadata-with-age-and-ordinal-timestamp.tsv")