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.