fcsannotate is a package for annotating FCS files with experimental metadata. It contains an API endpoint for annotating FCS files.
The endpoint currently labels the FCS file with the following keywords:
-
flow_cytometer: [name of the cytometer]
-
labeled_at: [timestamp generated at time of labelling]
To run server with the endpoint:
python fcsannotate/fcsannotate.py
PUT http://localhost/fcs_data/annotate/ [binary FCS file]
If successful, the endpoint returns a response with a status 200 and a labeled FCS file as a binary
in the response body.
Otherwise, it returns a 404 (file missing in request) or 500 status code (most likely, due to error
with FCS format).
Unit tests for annotating FCS files:
python fcsannotate/tests/test_annotate.py
Integration tests of annotation endpoint:
python fcsannotate/tests/test_annotate_endpoint.py
This package relies on Flask ('0.10.1) and was tested with Python: 2.7.1 (there were issues with fcsparser at Python 3.6.1 and Anaconda).
The package also uses the fork of fcsparser from https://github.com/NotableLabs/fcsparser (uses the write_file functionality).
I had to adjust a couple of imports in fcs_parser/__init__.py to make it work for me locally:
from ._version import version as __version__
from .api import parse
Please email me at sutee.dee@alumni.olin.edu with any questions.