Multiple Alignment Mapper
A python package for mapping genome-wide data onto multiple alignment of transposable elements.
This multiple alignment of THE1C for example:
can be overlayed by genome-wide data such as TF motif prediction, conservation socre, ChIP-exo mapped reads, common base frequencies, alternater allele frequencies, and more:
python3.10biopython1.83compress-pickle2.1.0cyvcf20.30.28h5py3.7.0logomaker0.8matplotlib3.8.4numpy1.21.5pandas1.3.5pybedtools0.10.0pybigwig0.3.23pysam0.22.0scipy1.7.3
To install this package, use the following command to install on a python environment:
pip install git+https://github.com/pkncsk/ma_mapper@experimentalma_mapper is ultimately a wrapper of various external packages, guiding them to work under under the multiple alignment mapping framework. The package itself is separated into modules and submodules based on their main functions on the framework. Notably, the data extraction and data mapping/overlay are streamlined into one module as shown below:
This package is licensed under the MIT License.