Arguments¶

usage: deltapd [-h] [--r_tree R_TREE] [--q_tree Q_TREE] [--metadata METADATA]
               [--msa_file MSA_FILE] [--out_dir OUT_DIR] [--max_taxa MAX_TAXA]
               [--qry_sep QRY_SEP] [--influence_thresh INFLUENCE_THRESH]
               [--diff_thresh DIFF_THRESH] [--k K] [--plot]
               [--ete3_scale ETE3_SCALE] [--cpus CPUS] [--debug]

I/O arguments (required)¶

--r_tree: path to the reference tree
--q_tree: path to the query tree
--metadata: path to the metadata file
--msa_file: path to the msa file used to infer the query tree
--out_dir: path to output directory

Query tree arguments (optional)¶

--max_taxa

if a ref taxon represents more than this number of qry taxa, ignore it

Default: 1000

--qry_sep

query taxon separator in query tree, e.g. taxon___geneid

Default: “___”

Outlier arguments (optional)¶

--influence_thresh

outlier influence threshold value [0,inf)

Default: 2

--diff_thresh

minimum change to base model to be considered an outlier

Default: 0.1

--k

consider the query taxa represented by the k nearest neighbours for each representative taxon

Default: 50

Plotting arguments (optional)¶

--plot

generate outlier plots (slow)

Default: False

--ete3_scale

pixels per branch length unit

Default: 200

Program arguments (optional)¶

--cpus

number of CPUs to use

Default: 1

--debug

output debugging information

Default: False