Getting help on an app#
app_help() function is a top-level import. It provides you with detailed help on an individual app. You pass the name of the app you want information on (see available apps) as a string. Below, I request help for the app
omit_degenerates by passing that name as a string.
from cogent3 import app_help app_help("omit_degenerates")
Overview -------- Excludes alignment columns with degenerate characters. Can accomodate reading frame. Options for making the app -------------------------- omit_degenerates_app = get_app( "omit_degenerates", moltype=None, gap_is_degen=True, motif_length=1, ) Parameters ---------- moltype : str molecular type, must be either DNA or RNA gap_is_degen : bool include gap character in degenerate character set motif_length : int sequences split into non-overlapping tuples of this size. If a tuple contains a degen character at any position the entire tuple is excluded Input type ---------- Alignment, ArrayAlignment Output type ----------- Alignment, ArrayAlignment, SerialisableType
The resulting vignette has multiple of sections.
“Overview” describes the app purpose.
“Options for making the app” shows how to create an app instance using
get_app()(Getting an app). It includes the positional and keyword arguments for the app.
“Parameters” lists the documentation describing the arguments.
“Input type” states what data types are acceptable as input to the app.
“Output type” states what data type will be generated by the app.