fcsy: Python package for processing FCS

fcsy is developed based on Data File Standard for Flow Cytometry Version FCS 3.1

Installation

$ pip install fcsy

for working with s3:

$ pip install fcsy[s3]

Usage

Write and read fcs based on Dataframe

>>> import pandas as pd
>>> from fcsy import DataFrame

>>> data = [[1.0,2.0,3.0],[4.0,5.0,6.0]]
>>> columns = pd.MultiIndex.from_tuples(list(zip('abc', 'ABC')), names=["short", "long"])
>>> df = DataFrame(data, columns=columns)
>>> df
short    a    b    c
long     A    B    C
0      1.0  2.0  3.0
1      4.0  5.0  6.0

>>> df.to_fcs('sample.fcs')
>>> df = DataFrame.from_fcs('sample.fcs', channel_type='multi')
>>> df
short    a    b    c
long     A    B    C
0      1.0  2.0  3.0
1      4.0  5.0  6.0

Work with fcs metadata

Read fcs channels

>>> from fcsy import read_channels

>>> read_channels('sample.fcs', channel_type='multi')
MultiIndex([('a', 'A'),
            ('b', 'B'),
            ('c', 'C')],
           names=['short', 'long'])

Rename channels

>>> from fcsy import rename_channels, read_channels

>>> rename_channels('sample.fcs', {'a': 'a_1', 'b': 'b_1'}, channel_type='short')
>>> read_channels('sample.fcs', channel_type='multi')
MultiIndex([('a_1', 'A'),
            ('b_1', 'B'),
            (  'c', 'C')],
           names=['short', 'long'])


>>> rename_channels('sample.fcs', {'A': 'A_1', 'C': 'C_1'}, channel_type='long')
>>> read_channels('sample.fcs', channel_type='multi')
MultiIndex([('a_1', 'A_1'),
            ('b_1',   'B'),
            (  'c', 'C_1')],
           names=['short', 'long'])

Read events number

>>> from fcsy import read_events_num

>>> read_events_num('sample.fcs')
2

Work with files on aws s3

All apis support s3 url with the format: s3://{bucket}/{key}.

<!-- >>> import boto3 >>> from moto import mock_s3 >>> mock = mock_s3() >>> mock.start() >>> s3 = boto3.client("s3", region_name="us-east-1") >>> _ = s3.create_bucket(Bucket='sample-bucket') -->

Write and read

>>> df.to_fcs('s3://sample-bucket/sample.fcs')
>>> df.from_fcs('s3://sample-bucket/sample.fcs', channel_type='multi')
short    a    b    c
long     A    B    C
0      1.0  2.0  3.0
1      4.0  5.0  6.0

Read channels

>>> read_channels('s3://sample-bucket/sample.fcs', channel_type='multi')
MultiIndex([('a', 'A'),
            ('b', 'B'),
            ('c', 'C')],
           names=['short', 'long'])

Read events number

>>> read_events_num('s3://sample-bucket/sample.fcs')
2

<!-- >>> mock.stop() -->

Documentation

The documentation is available on https://fcsy.readthedocs.io/

License

• Free software: MIT license

History

Consult the Releases page for fixes and enhancements of each version.