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]...

  -w, --width FLOAT               The width of the line. Defaults to 1.
  -p, --palette TEXT              Which color palette to use. Choose from boke
                                  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
  -t, --title TEXT                A title to display when plotting sequences
  --separate                      Whether to plot the visualizations
  -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
  --mode [seq|file|auto]          Whether to treat each sequence or file as
                                  the individual object. Defaults to automatic
  --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.