usage: __main__.py [-h] --intensities INTENSITIES [--array ARRAY]
                   [--mask MASK] [--genome GENOME] [--kmer-size KMER_SIZE]
                   [--max-gaps MAX_GAPS] [--outdir OUTDIR] [--prefix PREFIX]
                   [--pretty-logo]

Seed-and-wobble motif discovery from probe intensities + kmer occurrence
index.

options:
  -h, --help            show this help message and exit
  --intensities INTENSITIES
                        Path to probe intensity file
  --array ARRAY         Path to k-mer array file mapping k-mers to genomic
                        regions
  --mask MASK           Optional explicit 0/1 sequence mask for masked motif
                        discovery, e.g. 11111000011111. When supplied, the
                        mask defines the motif span and --genome is required;
                        the ordinary k-mer seed/extension path is left
                        unchanged.
  --genome GENOME       Genome FASTA used for masked motif discovery (--mask
                        mode)
  --kmer-size KMER_SIZE
                        k-mer size (default: 8)
  --max-gaps MAX_GAPS   Max number of wildcard ('.') positions when searching
                        seed patterns (default: 3; use 0 for exact k-mers
                        only)
  --outdir OUTDIR       Output directory (default: current directory)
  --prefix PREFIX       Output prefix (default: affinity_motif)
  --pretty-logo         Render a prettier motif logo (light gray background +
                        fixed DNA colors)
