v0.3.0

This release primarily contains functionality for the FIMO and TOMTOM algorithms. These algorithms, respectively, scan PWMs across long sequences to identify matches, and scan PWMs against each other to identify similar motifs. These two algorithms are invaluable for annotating results -- whether it's getting a sense for what motifs are in sequences when dissecting them using machine learning models, or identifying what motifs are present at seqlets. Hence, significant amounts of time have been put into optimizing the speed and memory efficiency of them.

These algorithms can be imported via

from tangermeme.tools.fimo import fimo

and

from tangermeme.tools.tomtom import tomtom

respectively. Each is a function that takes a set of motifs, and their second input, and some optional parameters, and returns the results.

Additionally, these functions make up the core of two command-line utilities that implement the algorithms and yield near-identical results to the MEME suite commands in only a fraction of the time. These can be used on the command-line via

tangermeme fimo -m <motif file> -s <sequence file> ...

and

tangermeme tomtom -q <motif file 1> -t <motif file 2> ...

However, sometimes you only have a hard sequence and you want to match it to a motif (like when, for instance, you're manually looking at motifs and want to get a sense for what the contiguous span of characters with high attributions are). Optionally, you can do something like

tangermeme tomtom -q ACGTTG -t <motif file 2>

or even

tangermeme tomtom -q ACGTTG

In the second case, the JASPAR 2024 motif set will be automatically downloaded and used in the future.