motif-mark is a program that searches introns and exons in a genetic sequence for motifs of interest in order to output an image that highlights the present motifs on a simple model of the gene.
- python 3+
- pycairo
- re
- matplotlib
User needs to supply two input files:
- A FASTA formatted file of gene sequences with exons denoted in uppercase letters and introns in lowercase
- A text file of motifs with 1 motif per line and no spaces
Example files of fasta and motifs can be found on github (listed as <example.file>).
Input on the command line requires the user to specify "-f" flag for the name of fasta file to be used and the "-m" flag for the name of the motif file to be used.
Example of how to run this script from terminal:
./motif_mark.py -f example.fasta -m example.motif
The script will generate a single-line fasta file as the program assumes the input was a multi-line fasta. This output can be disregarded if the input is already a single-line fasta.
The output of the script will be an SVG image outputted to the directory from which the script was run and be titled "motif_mark.svg".