phylogeny

This section is auto-generated from the help text for the chakin command phylogeny.

add_cvterms command

Usage:

chakin phylogeny add_cvterms [OPTIONS]

Help

Make sure required cvterms are loaded

Output

created cvterms

Options:

-h, --help  Show this message and exit.

gene_families command

Usage:

chakin phylogeny gene_families [OPTIONS]

Help

Adds an entry in the featureprop table in a chado database for each family a gene belongs to (for use in https://github.com/legumeinfo/lis_context_viewer/).

Output

None

Options:

--family_name TEXT  Restrict to families beginning with given prefix
--nuke              Removes all previous gene families data
-h, --help          Show this message and exit.

gene_order command

Usage:

chakin phylogeny gene_order [OPTIONS]

Help

Orders all the genes in the database by their order on their respective chromosomes in the gene_order table (for use in https://github.com/legumeinfo/lis_context_viewer/).

Output

None

Options:

--nuke      Removes all previous gene ordering data
-h, --help  Show this message and exit.

load_tree command

Usage:

chakin phylogeny load_tree [OPTIONS] NEWICK ANALYSIS_ID

Help

Load a phylogenetic tree (Newick format) into Chado db

Output

Number of inserted trees

Options:

--name TEXT            The name given to the phylotree entry in the database
                       (default=<filename>)
--xref_db TEXT         The name of the db to link dbxrefs for the trees
                       (default: "null")  [default: null]
--xref_accession TEXT  The accession to use for dbxrefs for the trees (assumed
                       same as name unless otherwise specified)
--match_on_name        Match polypeptide features using their name instead of
                       their uniquename
--prefix TEXT          Comma-separated list of prefix to be removed from
                       identifiers (e.g species prefixes when loading
                       OrthoFinder output)
-h, --help             Show this message and exit.