Importing FCS files into Flowkit
Closed this issue · 1 comments
Describe the bug
I am trying to read in my FCS files and I keep getting the following error:
IsADirectoryError: [Errno 21]
I copy the file path to the FCS files into fk.Sample('my specific file path') then I get the above error.
Code To Reproduce
Code to reproduce the behavior:
import flowkit as fk
import bokeh
import pandas as pd
fk.__version__
...
Expected behavior
I expect some notification that my FCS files are recognized
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
- OS: [Sonoma 14.4.1]
- Python version [3.11.5]
- FlowKit version [1.1.0]
Additional context
Hi,
I think the issue here is that you may be giving a directory path instead of a path to a single FCS file as the argument to the Sample
class. A Sample
instance represents a single FCS file. See the docs on the Sample
class for more information about the parameters.
Note there is also a utility function load_samples
that provides a convenient way to load multiple FCS files from a single directory path. See the doc on load_samples
here.
Let me know if that gets you past the error.
-Scott