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()
module | name | composable | doc | input type | output type |
---|---|---|---|---|---|
cogent3.app.io | pickle_it | True | Serialises data using pickle. | SerialisableType | bytes |
cogent3.app.io | unpickle_it | True | Deserialises pickle data. | bytes | SerialisableType |
cogent3.app.io | compress | True | Compresses bytes data. | bytes | bytes |
cogent3.app.io | decompress | True | Decompresses data. | bytes | bytes |
cogent3.app.io | to_primitive | True | convert an object to primitive python types suitable for serialisation | SerialisableType | SerialisableType |
... | ... | ... | ... | ... | ... |
cogent3.app.sample | min_length | True | Filters sequence collections / alignments by length. | Alignment, ArrayAlignment, SequenceCollection | Alignment, ArrayAlignment, SequenceCollection, SerialisableType |
cogent3.app.sample | fixed_length | True | Sample an alignment to a fixed length. | Alignment, ArrayAlignment | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.sample | omit_bad_seqs | True | Eliminates sequences from Alignment based on gap fraction, unique gaps. | Alignment, ArrayAlignment | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.sample | omit_duplicated | True | Removes redundant sequences, recording dropped sequences in seqs.info.dropped. | Alignment, ArrayAlignment, SequenceCollection | Alignment, ArrayAlignment, SequenceCollection, SerialisableType |
cogent3.app.sample | trim_stop_codons | True | Removes terminal stop codons. | Alignment, ArrayAlignment, SequenceCollection | Alignment, 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")
module | name | composable | doc | input type | output type |
---|---|---|---|---|---|
cogent3.app.io | load_aligned | True | Loads aligned sequences. Returns an Alignment object. | IdentifierType | Alignment, ArrayAlignment, SerialisableType |
cogent3.app.io | load_unaligned | True | Loads unaligned sequences. Returns a SequenceCollection. | IdentifierType | SequenceCollection, SerialisableType |
cogent3.app.io | load_tabular | True | Loads delimited data. Returns a Table. | IdentifierType | DictArray, DistanceMatrix, Table |
cogent3.app.io | load_json | True | Loads json serialised cogent3 objects from a json file. Returns whatever object type was stored. | IdentifierType | SerialisableType |
cogent3.app.io | load_db | True | Loads serialised cogent3 objects from a db. Returns whatever object type was stored. | IdentifierType | SerialisableType |
5 rows x 6 columns