This package provides a more pythonic wrapper around the MOODS Cpp // swig motif scanning tool.
There is also a notebook and some test data showing an example workflow. The deps for this are included as poetry development dependencies.
There are two main classes in the package, Scanner and Motif. Motif provides a
representation of a scanning matrix (for example a PWM, but not limited to just this) in
numpy format, alongside an ID field and a threshold. There are convenience functions
for loading PWMs from PFMs, and for calculating p-values (this just wraps MOODS).
The Scanner class takes a list of motifs, and builds a scanner, which will efficiently
scan a nucleotide sequence in one pass. This is a bit fiddly, since the scanner is not
strand-aware, and returns hits by motif order. I've taken a similar approach to the
moods-py script we use in regulation, but this is wrapped up so that the .scan()
method takes a pyfaidx.Sequence and outputs a list of TFBSs (small dataclass, effectively
just a BED row, tuples might be faster).
There is also a cli scan command, which should be very similar to the moods-py script,
but taking PWMs in json input, and some functions in readers.py for parsing MOODS
or JASPAR PWMs.
Currently the package doesn't have an easy way to use multiple cores: because Scanner
uses Swig objects, they can't be pickled. The most straightforward way would probably
be to create N processes to do the scanning, and just build a new Scanner in each
one.