Motif Mark assignment for BI625
motif-mark-oop.py is a Python script which uses object-oriented code to produce a visualization of nucleotide motifs on gene sequences.
The script must be run in a conda environment with pycairo installed.
-f: A FASTA file containing gene sequences- Up to 10 gene sequences
- Each sequence up to 1000 nucleotides in length
- Exons denoted as CAPITAL nucleotides, otherwise lowercase nucleotides
-m: A text file containing motif sequences- Up to 5 motifs
- One motif sequence per line
- Motifs should use IUPAC nucleotide notation
- The script will output a png figure displaying genes, exons, and motifs to scale.
- Genes are represented by a black line in the final image.
- Exons are represented by a semitransparent gray rectangle at the corresponding position on the gene line.
- Motifs are indicated by colored semitransparent markings along the black gene line.
- The script will identify motifs with degenerate nucleotides that are coded according to IUPAC notation.
- The script will identify overlapping motifs; the overlap will be visible with semitransparent colors on the final figure.