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# 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")) |
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