icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

bioinformatics, metabolomics, research, analysis, science
pip install icoshift==1.0



A versatile tool for the rapid alignment of 1D NMR spectra

This package is a Python implementation of the icoshift algorithm as described by Francesco Savorani and Giorgio Tomasi. It uses correlation shifting of spectral intervals and employs an FFT engine that aligns all spectra simultaneously.

The Matlab algorithm is demonstrated to be faster than similar methods found in the literature making full-resolution alignment of large datasets feasible and thus avoiding down-sampling steps such as binning. The algorithm uses missing values as a filling alternative in order to avoid spectral artifacts at the segment boundaries.

It has been converted to Python using SMOP followed by hand re-coding using test datasets to check output at various steps. Better (and more complicated) test cases to come.

The interface remains identical to the Matlab version at present.

Here Be Dragons

Conversion from one programming language to another is not straightforward. Particularly problematic from MATLAB to Python is the change from zero-based to one-based indexing. The implementation has been fixed to work and produce comparable output for all inputs, however issues with some datasets or settings may remain. Full tests to confirm equivalence to the MATLAB algorithm to follow.

But it works.


Thanks to Francesco Savorani and Giorgio Tomasi for the original neat and well documented algorithm.