Displaying installed apps

Apps perform functions ranging from multiple sequence alignment (e.g. progressive_align), to excluding alignment columns containing non-nucleotide characters (e.g. omit_degenerates) to performing maximum-likelihood evolutionary analyses (e.g. model).

from cogent3 import available_apps

available_apps()

package	name	composable	doc	input type	output type	licenses
piqtree	piq_build_tree	True		Alignment	PhyloNode	GPL-2.0-only
piqtree	piq_consensus_tree	True	Build a consensus tree, defaults to majority-rule consensus tree.		PhyloNode	GPL-2.0-only
piqtree	piq_fit_tree	True		Alignment	PhyloNode	GPL-2.0-only
piqtree	piq_jc_distances	True		Alignment	DistanceMatrix	GPL-2.0-only
piqtree	piq_model_finder	True	Find the models of best fit for an alignment using ModelFinder.	Alignment	ModelFinderResult	GPL-2.0-only
...	...	...	...	...	...	...
cogent3	uniformize_tree	True	Standardises the orientation of unrooted trees.	PhyloNode	PhyloNode, SerialisableType	BSD
cogent3	write_db	True	Write serialised objects to a database instance.	SerialisableType	DataMemberABC, Path, str	BSD
cogent3	write_json	True	Writes data in json format.	SerialisableType	DataMemberABC, Path, str	BSD
cogent3	write_seqs	True	Write sequences in standard formats.	Alignment, SequenceCollection	DataMemberABC, Path, str	BSD
cogent3	write_tabular	True	Writes tabular data in text format supported by the cogent3 Table object.	DictArray, DistanceMatrix, Table	DataMemberABC, Path, str	BSD

Top 5 and bottom 5 rows from 54 rows x 7 columns

The name_filter argument can be used to display only the apps that match a string. For example, to display all the loader apps

available_apps(name_filter="load")

package	name	composable	doc	input type	output type	licenses
cogent3	load_aligned	True	Loads aligned sequences. Returns an Alignment object.	DataMemberABC, Path, str	Alignment, SerialisableType	BSD
cogent3	load_db	True	Loads serialised cogent3 objects from a db. Returns whatever object type was stored.	DataMemberABC, Path, str	SerialisableType	BSD
cogent3	load_json	True	Loads json serialised cogent3 objects from a json file. Returns whatever object type was stored.	DataMemberABC, Path, str	SerialisableType	BSD
cogent3	load_tabular	True	Loads delimited data. Returns a Table.	DataMemberABC, Path, str	DictArray, DistanceMatrix, Table	BSD
cogent3	load_unaligned	True	Loads unaligned sequences. Returns a SequenceCollection.	DataMemberABC, Path, str	SequenceCollection, SerialisableType	BSD

5 rows x 7 columns

Note

The first column lists the package providing the app.