CLI Reference¶
Squiggle’s CLI is documented fully below. Note that this reference is available
at any time by invoking the squiggle --help
command.
$ squiggle --help
Usage: squiggle [OPTIONS] [FASTA]...
Options:
-w, --width FLOAT The width of the line. Defaults to 1.
-p, --palette TEXT Which color palette to use. Choose from boke
h.pydata.org/en/latest/docs/reference/palett
es.html. Defaults to Category10.
--color / --no-color Whether to plot the visualizations in color.
--hide / --no-hide Whether to hide sequences when clicked in
the legend. Defaults to false.
--bar / --no-bar Whether to show a progress bar when
processing multiple sequences. Defaults to
true.
-t, --title TEXT A title to display when plotting sequences
together.
--separate Whether to plot the visualizations
separately.
-c, --cols INTEGER The number of columns when plotting
separately. Defaults to a the closest to
square layout as possible.
--link-x / --no-link-x Whether to link the x axes for separate
plotting. Defaults to true.
--link-y / --no-link-y Whether to link the y axes for separate
plotting. Defaults to false.
-o, --output FILE The output file for the visualization. If
not provided, will open visualization in
browser. The filetype must be .html
--offline Whether to include the resources needed to
plot offline when outputting to file.
Defaults to false.
--method [squiggle|gates|yau|yau-bp|randic|qi]
The visualization method.
-d, --dimensions WIDTH HEIGHT The width and height of the plot,
respectively. If not provided, will default
to 750x500.
--skip / --no-skip Whether to skip any warnings. Defaults to
false.
--mode [seq|file|auto] Whether to treat each sequence or file as
the individual object. Defaults to automatic
selection.
--legend-loc [top_left|top_center|top_right|center_right|bottom_right|bottom_center|bottom_left|center_left|center]
Where to put the legend, if applicable.
Defaults to top left.
--output-backend [canvas|svg|webgl]
Which output backend to use while plotting.
Defaults to canvas.
-s, --downsample INTEGER The downsampling factor. Useful for handling
large sequences. Default value is 1.
-h, --help Show this message and exit.