A package for processing FCS files
Project description
fcsy
A package for processing FCS files.
- Free software: MIT license
Installation
$ pip install fcsy
Usage
Use the pandas flavor api fcsy.DataFrame
which
has all the features of pandas DataFrame plus the fcs io (New in v0.5.0).
API (ver >= 0.5.0)
DataFrame.from_fcs(path, channel_type='short')
Read fcs file to dataframe
path | path to the input fcs |
channel_type | "short" | "long" | "multi". Read short or long channels to the dataframe columns. In "multi" mode both channels are read as a pandas MultiIndex |
return | DataFrame |
Example:
from fcsy import DataFrame
df = DataFrame.from_fcs('sample1.fcs', channel_type='multi')
DataFrame.to_fcs(path)
Write dataframe to fcs file. 'short' and 'long' channels will be written separately if pandas MultiIndex is used as the columns. Otherwise 'short' and 'long' channels will be the same writen from the columns.
Example:
import numpy as np
from fcsy import DataFrame
df = DataFrame(np.random.rand(10, 4)), columns=list('ABCD'))
df.to_fcs('sample1.fcs')
Old API
Write a data frame to fcs. df.columns is written to both short and long names of the fcs.
from fcsy import write_fcs
write_fcs(df, 'output_file')
Write to fcs with "long name". df.columns and long_names are written to short and long names of the fcs.
write_fcs(df, 'output_file', long_names=['a','b','c'])
Read a fcs file to pandas DataFrame.
from fcsy import read_fcs
df = read_fcs('input_file')
Read a fcs file with "long name"
df = read_fcs('input_file', name_type='long')
# or only read the names
from fcsy import read_fcs_names
long_names = read_fcs_names('input_file', name_type='long')
Write a data frame to fcs. df.columns is written to both short and long names of the fcs.
from fcsy import write_fcs
write_fcs(df, 'output_file')
Write to fcs with "long name". df.columns and long_names are written to short and long names of the fcs.
write_fcs(df, 'output_file', long_names=['a','b','c'])
Credits
This package was created with Cookiecutter* and the audreyr/cookiecutter-pypackage
* project template.
Cookiecutter
: https://github.com/audreyr/cookiecutter
audreyr/cookiecutter-pypackage
: https://github.com/audreyr/cookiecutter-pypackage
======= History
0.1.0 (2018-12-18)
- First release on PyPI.
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