Adds an "age in years" column to a QIIME 2 sample metadata file

add_age_column_to_metadata.py

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

subject_id = "HOST SUBJECT ID"
subject_birthday = "HOST BIRTHDAY"
subject_birthday_datetime = parse(subject_birthday)
age_col_name = "subject_age_years"

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

m_df[age_col_name] = 0

for sample_id in m_df.index:
    # We only compute age for samples with the specified host_subject_id
    if m_df.loc[sample_id, "host_subject_id"] == subject_id:
        # Parse sample timestamp
        sample_timestamp = m_df["collection_timestamp"][sample_id]
        sample_datetime = parse(sample_timestamp)

        rd = relativedelta(sample_datetime, subject_birthday_datetime)
        # Sanity check: the subject should never be negative years old
        if rd.years > 0:
            m_df.loc[sample_id, age_col_name] = str(rd.years)
        else:
            raise ValueError(
                "Sample {} has a collection_timestamp, {}, occurring before "
                "the subject_birthday of {}.".format(
                    sample_id, sample_timestamp, subject_birthday
                )
            )
    else:
        m_df.loc[sample_id, age_col_name] = "not applicable"

Metadata(m_df).save("output_metadata.tsv")