Skip to main content

A package for processing FCS files

Project description

image image image image image

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}.

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

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

fcsy-0.10.0.tar.gz (22.4 kB view hashes)

Uploaded source

Built Distribution

fcsy-0.10.0-py2.py3-none-any.whl (11.0 kB view hashes)

Uploaded py2 py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page