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STAR file reading and writing in python.

Project description

starfile

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starfile is a Python implementation of the STAR file format designed principally for compatibility with RELION format STAR files.

It allows STAR files to be created and opened easily using a very simple API, exposing data blocks as pandas DataFrame objects.

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

Features

  • Easy to install and use
  • Simple API for reading of STAR files as pandas DataFrame objects
  • Simple API for writing of STAR files from pandas DataFrame objects

Installation

Installation is available directly from the Python package index

pip install starfile

Currently python>=3.8 is supported.

Usage

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 dict of DataFrame objects.
  • If you would like to always return a dict, you can use the always_dict=True keyword argument

Writing STAR files

DataFrame objects (or dicts or lists of dataframes) can be written to STAR files using starfile.write

>>> 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_format keyword argument (default %.6f)
  • data block headers are of format data_<key> where key is the dictionary key if a dict is passed, df.name if a DataFrame or list of DataFrames is passed

Interactive usage

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.

starfile tests/data/loop_block.star
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.

License

The project is released under the BSD 3-Clause License

Testing

The project is tested using pytest. To run tests, simply run pytest in the tests directory

Known Issues

  • 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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