This repository houses code that maps TFBS onto alignments. The purpose is to identify where TFBS are in an alignment. There are currently three aspects of the code, located in /code
directory.
map+motif.py
script that can be implemented in command line. motif_scoring_and_extraction.ipynb
that is a jupyter notebook of the script for interactive coding and visualization /D3_vis
portion, which is a working project to visualize TFBS interactively in the browser. map_motif.py
map_motif.py
is a python script that has two inputs.
File Inputs:
Arguments:
File Outputs:
-.csv
file that outputs found TFBSs at each position, if any, in alignment.
Output data frame includes:
The output file will be saved in directory script was ran.
Example output file: map_motif-alignment.fa-motif.fm.csv
python map_motif.py alignment.fa motif.fm 3.2