gettingstarted.md

Getting started

Quick links

• About ma_mapper
• Dependencies
• Installation
• Package structure
• Package documentations

Under construction

• Tutorials
• API references

About ma_mapper

ma_mapper is a python package for mapping genome-wide data onto multiple alignment of transposable elements. The main function of this package is to work as a wrapper for other biological data file handlers such as biopython to steamline multiple alignment data overlay. The output of this package is a numerical numpy matrix, which can be easily used for visualization by matplotlib or seaborn.

Dependencies

General package

• python 3.10
• compress-pickle 2.1.0
• h5py 3.7.0
• numpy 1.21.5
• pandas 1.3.5
• scipy 1.7.3

Genome-wide data file handler

• biopython 1.83
• pybedtools 0.10.0
• pybigwig 0.3.23
• pysam 0.22.0
• cyvcf2 0.30.28

Visualization

• logomaker 0.8
• matplotlib 3.8.4

Installation

To install this package, use the following command to install on a python environment:

pip install git+https://github.com/pkncsk/ma_mapper@experimental

Package structure

ma_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:

Package documentation

Documentaion for general usages and function parameters.