ooca-motif-mark.md

Motif Mark Plan

Generate plan of attack for creating visual of motif locations within a series of sequences.

List of classes

• Read

  • takes each sequence from the fasta
  • some kind of unique identifier
  • keep track of which motifs match where
  • location of exons
  • location of introns

• Motif

  • contains motif sequence
  • functionality for ambiguous nucleotides

• Gene - not clear on read vs. gene?

List of functions

• pycairo drawing function
• argparse
  • -f: fasta file
  • -m: motifs file
• read through fasta
• read through motif file
• function to match motifs within reads/genes