STAR file reading and writing in python.
It allows STAR files to be created and opened easily using a very simple API, exposing data blocks as pandas
This library aims to allow users and developers to read and write STAR files in Python as easily as possible as well as to encourage further analysis of data within the scientific Python (SciPy) ecosystem.
You can use it interactively to inspect/explore files or in scripts and larger software packages to provide basic STAR file I/O functions.
The STAR file: a new format for electronic dataframes transfer and archiving J. Chem. Inf. Comput. Sci. 1991, 31, 2, 326–333 Publication Date: May 1, 1991 https://doi.org/10.1021/ci00002a020
- Easy to install and use
- Simple API for reading of STAR files as pandas
- Simple API for writing of STAR files from pandas
Installation is available directly from the Python package index
pip install starfile
3.8 is supported. You can check your
python version with
We recommend installing into a virtual environment for use in your projects.
Reading STAR files
To open a STAR file
>>> import starfile >>> df = starfile.read('tests/dataframes/one_loop.star') >>> df rlnCoordinateX rlnCoordinateY ... rlnAngleTilt rlnAnglePsi 0 1572.444 1084.500 ... 0 0 1 1507.500 1104.357 ... 0 0 2 1512.432 973.500 ... 0 0 3 1560.385 1063.500 ... 0 0 4 1537.500 1060.500 ... 0 0 ... ... ... ... ... 1360 1078.500 796.500 ... 0 0 1361 1075.500 784.500 ... 0 0 1362 1080.531 796.500 ... 0 0 1363 1045.992 737.411 ... 0 0 1364 1053.530 745.500 ... 0 0 [1365 rows x 12 columns]
- Opening STAR files containing multiple dataframes blocks will return a
dictof DataFrame objects.
- If you would like to always return a
dict, you can use the
Writing STAR files
DataFrame objects (or dicts or lists of dataframes) can be written to STAR files using
>>> starfile.write(df, 'tests/dataframes/cars.star')
Produces a STAR file which looks like
# Created by the starfile python package (version 0.1) on 18/06/2020 13:26:32 data_cars loop_ _Brand #1 _Price #2 Honda_Civic 22000 Toyota_Corolla 25000 Ford_Focus 27000 Audi_A4 35000
- floating point format can be specified by the
float_formatkeyword argument (default
- data block headers are of format
data_<key>where key is the dictionary key if a
DataFrameor list of
DataFrames is passed
You can also use
starfile as an interactive command line tool for quick
and dirty data analysis.
This functionality can be installed using pip:
pip install starfile[cli]
Note that with certain shells (e.g.
zsh) you may need to use
pip install 'starfile[cli]' to avoid unwanted shell expansion of the
square bracket syntax.
You can then call
starfile <my_file>.star to be dropped into an interactive
Python console with access to your data.
Python 3.9.6 (default, Aug 18 2021, 12:38:10) Type 'copyright', 'credits' or 'license' for more information IPython 7.27.0 -- An enhanced Interactive Python. Type '?' for help. === Starfile === - access your data with `star` - write it out with `write(...)`
Both matplotlib and seaborn are available for plotting your data in this interactive shell.
The project is released under the BSD 3-Clause License
The project is tested using pytest.
To run tests, simply run
pytest in the
- Cannot handle more than one loop in a data block as found in mmCIF files, please use GEMMI in these cases
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