pyryotype 0.0.5

Draw an ideogram of either HG38 or CHM13 contigs in a matplotlib axes object.

pyryotype

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Table of Contents

• pyryotype
  • Installation
  • Example usage
  • License
  • Cytoband data

Installation

    pip install ideogram

Example usage

from pyryotype import GENOME, plot_ideogram
from matplotlib import pyplot as plt
fig, axes = plt.subplots(
    ncols=1,
    nrows=22,
    figsize=(11, 11),
    facecolor="white",
)
genome = GENOME.CHM13
for ax, contig_name in zip(axes, range(1, 23)):
    chromosome = f"chr{contig_name}"
    plot_ideogram(ax, target=chromosome, genome=genome)
fig.savefig("ideogram.png", dpi=300)

Will output:

Coverage plotting is designed to be used with the output of Mosdepth. The following example uses the output of mosdepth to plot the coverage of the first 10Mb of chromosome 1 of the CHM13 genome.

from pyryotype import GENOME, plot_coverage
from matplotlib import pyplot as plt
fig, ax = plt.subplots(
    figsize=(11, 2),
    facecolor="white",
)
plot_coverage(
    ax,
    "HG01280.regions.bed.gz",
    target="chr1",
    start=0,
    end=10000000,
)
fig.savefig("coverage.png", dpi=300)

License

pyryotype is distributed under the terms of the MIT license.

Cytoband data

• HG38 - Nushell, will have to be adapted for bash curl -L "https://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz" | gzip -d - | rg -Ne "^chr\\d+\t" | save cytoBand_HG38.tsv
• CHM13 - bash yay curl -L http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v2.0/download/chm13v2.0_cytobands_allchrs.bed.gz | gzip -d - > cytobands_chm13.bed