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()
packagenamecomposabledocinput typeoutput type
piqtreepiqtree_fitTrueAlignment, ArrayAlignmentPhyloNode, SerialisableType
piqtreepiqtree_jc_distsTrueAlignment, ArrayAlignmentPhyloNode, SerialisableType
piqtreepiqtree_mfinderTrueFind the models of best fit for an alignment using ModelFinder.Alignment, ArrayAlignmentModelFinderResult, SerialisableType
piqtreepiqtree_njTrueConstruct a neighbour joining tree from a pairwise distance matrix.DistanceMatrixPhyloNode
piqtreepiqtree_phyloTrueAlignment, ArrayAlignmentPhyloNode, SerialisableType
..................
cogent3uniformize_treeTrueStandardises the orientation of unrooted trees.PhyloNode, TreeNodePhyloNode, SerialisableType, TreeNode
cogent3write_dbTrueWrite serialised objects to a database instance.SerialisableTypeIdentifierType
cogent3write_jsonTrueWrites data in json format.SerialisableTypeIdentifierType
cogent3write_seqsTrueWrite sequences in standard formats.Alignment, ArrayAlignment, SequenceCollectionIdentifierType
cogent3write_tabularTrueWrites tabular data in text format supported by the cogent3 Table object.DictArray, DistanceMatrix, TableIdentifierType

Top 5 and bottom 5 rows from 52 rows x 6 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")
packagenamecomposabledocinput typeoutput type
cogent3load_alignedTrueLoads aligned sequences. Returns an Alignment object.IdentifierTypeAlignment, ArrayAlignment, SerialisableType
cogent3load_dbTrueLoads serialised cogent3 objects from a db. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3load_jsonTrueLoads json serialised cogent3 objects from a json file. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3load_tabularTrueLoads delimited data. Returns a Table.IdentifierTypeDictArray, DistanceMatrix, Table
cogent3load_unalignedTrueLoads unaligned sequences. Returns a SequenceCollection.IdentifierTypeSequenceCollection, SerialisableType

5 rows x 6 columns

Note

The first column lists the package providing the app.