Tool to generate pcl type file

rbutleriii · October 28, 2020, 5:15pm

Hi, working through the HUMAnN tutorial, and the humann_barplot requires the metadata to be included in the file with the abundance data. Is there already a script that efficiently adds the metadata fields to the top to make that *.pcl file?

franzosa · November 6, 2020, 3:26pm

Hmm… I don’t think there is one packaged with the biobakery tools. It is basically a “join” operation on the sample names (which should be conserved between the feature file and the metadata file). I use this script from my personal codebase (which should be public) to complete this task:

github.com

franzosa/zopy/blob/master/scripts/merge_tables.py

#!/usr/bin/env python

import os
import sys
import re
import glob
import argparse

from zopy.table2 import table, c_strNA, nesteddict2table
from zopy.utils import warn

# ---------------------------------------------------------------
# argparse 
# ---------------------------------------------------------------

parser = argparse.ArgumentParser()
parser.add_argument( 
    "tables",
    nargs="+",
    help="one or more data tables",

This file has been truncated. show original

Passing the metadata table via the -m flag will attach it to the top of a set of merged tables (or a single table).

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Tool to generate pcl type file

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