This script was created in order to provide a tool that would enable the visualization of motifs within gene sequences. Given an input fasta file, and a reference file containing motifs to search for, the script will produce a scaled image containing the locations of the motifs provided.
To use this script, execute:
motif-mark-oop.py
with the following arguments:
-f --fasta file: input fasta file containing either RNA and/or DNA sequence reads. The script identifies exons based on character captilization.
-m --motifs file: file containing motifs to search for within each gene. Motif file should contain 1 motif per line and can handle any combination of pyrimadines and/or purines (i.e 'r' and 'y' are acceptable characters for purine and pyrimidine searching, respectively).
See example input motif file labled Fig_1_motifs.txt and fasta file labeled Figure_1.fasta for reference.
See Figure_1.png below for an example of the output of the script.
