API Reference

CLI cmds

dreem draw

dreem draw [OPTIONS]

Options

--inpt <inpt>

Path to a dreem output format file. Can be specified multiple times.

--out-dir <out_dir>

Where to output all finished files

--flat, --no-flat

Flatten the output folder structure. This names your files [reference]__[section]__[plot_name].html

-c, --coords <coords>

Reference name, 5’ end, and 3’ end of a section; coordinates are 1-indexed and include both ends

--section <section>

Section to draw. Can be specified multiple times.

-mf, --mutation_fraction

Plot mutation_fraction plot. See Plots/gallery.

-mfi, --mutation_fraction_identity

Plot mutation_fraction_identity plot. See Plots/gallery.

-bc, --base_coverage

Plot base_coverage plot. See Plots/gallery.

-mib, --mutations_in_barcodes

Plot mutations_in_barcodes plot. See Plots/gallery.

-mprps, --mutation_per_read_per_reference

Plot mutation_per_read_per_reference plot. See Plots/gallery.

Python args

dreem.draw.run(inpt: tuple[str] = (), *, flat: list = True, out_dir: str = './output', coords: tuple = (), section: str = ('full',), mutation_fraction: bool = True, mutation_fraction_identity: bool = True, base_coverage: bool = True, mutations_in_barcodes: bool = False, mutation_per_read_per_reference: bool = True)

Run the draw command.

Parameters

• inpt (tuple) – Path to a dreem output format file. Can be specified multiple times. [positional or keyword, default: ()]

• flat (list) – Flatten the output folder structure. This names your files [reference]__[section]__[plot_name].html [keyword-only, default: True]

• out_dir (str) – Where to output all finished files [keyword-only, default: ‘./output’]

• coords (tuple) – Reference name, 5’ end, and 3’ end of a section; coordinates are 1-indexed and include both ends [keyword-only, default: ()]

• section (str) – Section to draw. Can be specified multiple times. [keyword-only, default: (‘full’,)]

• mutation_fraction (bool) – Plot mutation_fraction plot. See Plots/gallery. [keyword-only, default: True]

• mutation_fraction_identity (bool) – Plot mutation_fraction_identity plot. See Plots/gallery. [keyword-only, default: True]

• base_coverage (bool) – Plot base_coverage plot. See Plots/gallery. [keyword-only, default: True]

• mutations_in_barcodes (bool) – Plot mutations_in_barcodes plot. See Plots/gallery. [keyword-only, default: False]

• mutation_per_read_per_reference (bool) – Plot mutation_per_read_per_reference plot. See Plots/gallery. [keyword-only, default: True]