fcs_to_csv.py

# Flow Cytometry Standard file format --> csv
# https://stackoverflow.com/questions/70348405/how-to-convert-lmd-file-to-csv-flow-cytometry-data
# https://pypi.org/project/fcsparser/

"""
This script collects all files in the same directory as the script (or cwd) with 
the file ending "fcs". These files are assumed to be in the Flow Cytometry Standard file format 
anhd converted to CSV using pandas, and fcsparser. To install requirements:

pip install fcsparser pandas
"""


import pandas as pd
import fcsparser
from pathlib import Path

for pth in Path(".").glob("*.fcs"):
    print(pth)
    meta = fcsparser.parse(pth,meta_data_only=True)
    meta, data = fcsparser.parse(pth, meta_data_only=False, reformat_meta=True)
    df = pd.DataFrame(data)
    df.to_csv(pth.with_suffix(".csv"))