expressionable Python Module
The official repository for the expressionable Python module, which allows for:
- Transforming tabular data sets from one format to another.
- Querying large data sets to filter out useful data.
- Selecting additional columns/features to include in the resulting data set.
- Merging data sets of various formats into a single file.
- Gzipping resulting data sets, as well as the ability to read gzipped files.
Click for information on the ExpressionAble command-line tool, which combines the features of ExpressionAble with the ease and speed of the command-line!
Basic use is described below, but see the full documentation on Read the Docs.
pip install expressionable
After installing, import the ExpressionAble class with
from expressionable import ExpressionAble. An ExpressionAble object
represents the file to be transformed. It is then transformed using the
export_filter_results method. Here is a simple
example of file called
input_file.tsv being transformed into an HDF5 file called
output_file.h5, while filtering
the data on sex and age:
from expressionable import ExpressionAble my_expressionable = ExpressionAble("input_file.tsv") my_expressionable.export_filter_results("output_file.h5", filters="Sex == 'M' and Age > 40")
Note that the type of file being read and exported to were not stated explicitly but inferred by ExpressionAble based on
the file extensions provided. If necessary,
output_file_type can be named explicitly.
We welcome contributions that help expand ExpressionAble to be compatible with additional file formats. If you are interested in contributing, please follow the instructions here.
Currently Supported Formats
Future Formats to Support
We are working hard to expand ExpressionAble to work with even more file formats! Expect the following formats to be included in future releases:
- Fixed-width files (fwf)
- Genomic Data Commons clinical XML