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Read chromatography and mass spectrometry binary files.

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rainbow

PyPI Documentation Status PyPI - Downloads

rainbow provides programmatic access to the raw data encoded in chromatography and mass spectrometry binary files. This library supports the following vendors and detectors:

Agilent .D

  • .uv - UV spectrum (supports incomplete files)
  • .ch - UV, FID, CAD, and ELSD channels
  • .ms - MS (supports incomplete files)
  • MSProfile.bin - HRMS

Waters .raw

  • CHRO - CAD and ELSD, as well as miscellaneous analog data
  • FUNC - UV and MS

There is documentation for rainbow that also details the structure of each binary file format.

Installation

pip install rainbow-api

Usage

The easiest way to get started is to give rainbow a directory path. Assume that we have a directory mydata.D that contains a binary file DAD1.uv with UV data.

import rainbow as rb
datadir = rb.read("mydata.D")
datafile = datadir.get_file("DAD1A.uv")

Here, the datadir DataDirectory object contains a DataFile object for DAD1A.uv. The raw UV data is contained in numpy arrays that are attributes of datafile. Users may find the following particularly useful:

  • datafile.xlabels - 1D numpy array with retention times
  • datafile.ylabels - 1D numpy array with wavelengths
  • datafile.data - 2D numpy array with absorbances

There is a tutorial available. There are also example snippets for basic tasks. Or just check out the full API.

Contents

  • rainbow/ contains the code of the Python library.
  • docs/ contains code for generating documentation. To build documentation locally, you will need to install the sphinx and sphinx-rtd-theme packages. Then, move to the docs/ directory and run make html. The docpages will be generated under docs/_build.
  • tests/ contains unit tests for the library. These can be run with python -m unittest.

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Read chromatography and mass spectrometry binary files.

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