rdat-kit 1.7.0

RDATKit is a utility library for reading and writing RDAT files that describe RNA structure mapping experiments

RDATKit (RNA Dataset ToolKIT)

RDATkit is a set of tools for parsing, analyzing, and publishing data of RNA chemical footprinting assays. It allows researchers to share their data using community standard formats, and helps them publish their results on indexable and shareable databases.

RDATKit is a package provides a set of Python and MATLAB scripts that facilitate saving and loading data to and from files with RDAT format. It also supports the ISATAB file format.

Installation

MATLAB

• Download the zip or tar file of the repository and unpack; or

git clone https://github.com/ribokit/RDATKit.git

• In MATLAB, go to "Set Path". Then "Add with Subfolders" of the target path/to/RDATKit/MATLAB/.

Python

To install RDATKit, simply:

pip install rdat_kit

RDATKit requires the following Python packages as dependencies, all of which can be installed through pip.

numpy >= 1.8.0
scipy >= 0.13.0
xlrd >= 0.9.2
xlwt >= 1.0.0

Command-line interface

As of v1.7.0, rdat_kit registers a CLI with two subcommands:

# Validate one or more RDAT files (parses + runs RDATFile.validate())
rdat_kit validate path/to/entry.rdat

# Emit a Jekyll/RMDB front-matter .md stub for use in
# https://github.com/DasLab/rmdb.github.io
rdat_kit to_md path/to/entry.rdat > _entries/RMDB_ID.md

validate exits with code 0 on success, 1 on parse failure, 2 if RDATFile.validate() returned warnings. to_md derives the RMDB_ID from the filename (<PREFIX>_<CHEM>_<NNNN> pattern) and accepts --rmdb-id to override.

Documentation

Documentation is available at https://ribokit.github.io/RDATKit/.

License

Copyright © of RDATKit Source Code is described in LICENSE.md.

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Developed by Das lab, Leland Stanford Junior University.