fcswrite

0.6.4 verified Fri May 01 auth: no python maintenance

A lightweight library for writing Flow Cytometry Standard (FCS) files from Python. Current version 0.6.4, requires Python >=3.6. The library is in maintenance mode with infrequent releases.

pip install fcswrite

Common errors

error AttributeError: module 'fcswrite' has no attribute 'write_fcs' ↓

cause Incorrect import: using 'import fcswrite' instead of 'from fcswrite import fcswrite'

fix

Use: from fcswrite import fcswrite

error TypeError: write_fcs() missing 1 required positional argument: 'data' ↓

cause Calling write_fcs without all required arguments (filename, chnames, data).

fix

Provide all three positional arguments: write_fcs('output.fcs', ['FSC','SSC'], data_matrix)

Warnings

gotcha The function is named 'write_fcs' but must be accessed via 'fcswrite.write_fcs' after 'from fcswrite import fcswrite'. ↓

fix Use: from fcswrite import fcswrite; fcswrite.write_fcs(...)

gotcha The library does not support writing FCS 3.0 or later versions; it only writes FCS 2.0 files. ↓

fix For FCS 3.0+ support, consider other libraries like 'flowio' or 'fcsy'.

Imports

fcswrite
wrong
```
import fcswrite
```
correct
```
from fcswrite import fcswrite
```
fcswrite is a module, not a package; the correct import is 'from fcswrite import fcswrite' to get the write_fcs function.

Quickstart

Minimal example to write an FCS file with two channels and three events.

from fcswrite import fcswrite
import numpy as np

# Create some data (events x channels)
data = np.array([[1, 2], [3, 4], [5, 6]], dtype=np.float32)

# Channel names
chnames = ['FSC', 'SSC']

# Write FCS file
fcswrite.write_fcs('test.fcs', chnames, data)
print('FCS file written successfully.')