Logo

coralsnake logo plots a DNA/RNA sequence logo from a set of motif sequences. The scoring engine is pure numpy; the renderer needs matplotlib (the plot extra).

Usage

coralsnake logo -m ACGT -m ACGG -m CCGT -o logo.png

Per-motif weights from a file (seq<TAB>count):

cat motifs.tsv
# ACGT  5
# ACGG  3
coralsnake logo -i motifs.tsv -o logo.svg

Options

Option	Description
-m, --motifs	Motif sequence(s). Repeatable or comma-separated.
-i, --input	Input file, one motif per line (seq<TAB>count).
-o, --output	Output image (png/svg). required.
-w, --weights	Comma-separated per-motif weights.
--t2u/--no-t2u	Convert T to U (default on).
--2bit/--no-2bit	Use 2-bit information logo (default on).
--normed	Normalize letter heights to sum to 1.

Python API

from coralsnake import Mlogo

m = Mlogo(motifs=["ACGT", "ACGG", "CCGT"], to2bit=True)
m.plot(ax)  # requires matplotlib (plot extra)