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()
modulenamecomposabledocinput typeoutput type
cogent3.app.iopickle_itTrueSerialises data using pickle.SerialisableTypebytes
cogent3.app.iounpickle_itTrueDeserialises pickle data.bytesSerialisableType
cogent3.app.iocompressTrueCompresses bytes data.bytesbytes
cogent3.app.iodecompressTrueDecompresses data.bytesbytes
cogent3.app.ioto_primitiveTrueconvert an object to primitive python types suitable for serialisationSerialisableTypeSerialisableType
..................
cogent3.app.samplemin_lengthTrueFilters sequence collections / alignments by length.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.samplefixed_lengthTrueSample an alignment to a fixed length.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampleomit_bad_seqsTrueEliminates sequences from Alignment based on gap fraction, unique gaps.Alignment, ArrayAlignmentAlignment, ArrayAlignment, SerialisableType
cogent3.app.sampleomit_duplicatedTrueRemoves redundant sequences, recording dropped sequences in seqs.info.dropped.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType
cogent3.app.sampletrim_stop_codonsTrueRemoves terminal stop codons.Alignment, ArrayAlignment, SequenceCollectionAlignment, ArrayAlignment, SequenceCollection, SerialisableType

Top 5 and bottom 5 rows from 54 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")
modulenamecomposabledocinput typeoutput type
cogent3.app.ioload_alignedTrueLoads aligned sequences. Returns an Alignment object.IdentifierTypeAlignment, ArrayAlignment, SerialisableType
cogent3.app.ioload_unalignedTrueLoads unaligned sequences. Returns a SequenceCollection.IdentifierTypeSequenceCollection, SerialisableType
cogent3.app.ioload_tabularTrueLoads delimited data. Returns a Table.IdentifierTypeDictArray, DistanceMatrix, Table
cogent3.app.ioload_jsonTrueLoads json serialised cogent3 objects from a json file. Returns whatever object type was stored.IdentifierTypeSerialisableType
cogent3.app.ioload_dbTrueLoads serialised cogent3 objects from a db. Returns whatever object type was stored.IdentifierTypeSerialisableType

5 rows x 6 columns