semvec/pypi-packages huggingface dataset:
motevoparser 0.0.2
Simple Python MotEvo parser.
License: MIT
Keywords: MotEvo,parser,binding,sites

# motevoparser

Simple Python parser for MotEvo files.

[MotEvo](https://pubmed.ncbi.nlm.nih.gov/22334039/)<sup>1</sup> is a Bayesian probabilistic model for prediction of transcription factor binding sites (TFBSs) for a given set of position weight matrices (PWMs) and DNA sequences. It was developed by van Nimwegen lab at the Biozentrum (University of Basel, Switzerland) and it can be acquired [here](https://swissregulon.unibas.ch/sr/software).

This repository contains the source code for a simple Python package for parsing MotEvo output files.

MotEvo produces 2 files: `sites` and `priors` file. Usage of the package is simple. For a given MotEvo sites file stored at `/path/to/sites_MOTIF.wm` by calling:

```
from motevoparser import parse_sites

df_sites = parse_sites('/path/to/sites_MOTIF.wm') # Motif binding sites
df_priors = parse_sites('/path/to/priors_MOTIF.wm') # Final file with priors

```

you get a Pandas data frame containing parsed data from the MotEvo run. Further manipulation with the dataframe allows getting motif binding density on all sequences, number of binding sites, number of different species from alignment used, etc.

## References

1. Arnold, Phil, et al. "MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences." Bioinformatics 28.4 (2012): 487-494.