augur import

Import analyses into augur pipeline from other systems

usage: augur import [-h]
                    Import analyses into augur pipeline from other systems ...

TYPE

Import analyses into augur pipeline from other systems

Possible choices: beast

Sub-commands

beast

Parse a BEAST MCC tree for further analysis in augur or export for auspice v2+ (using augur export v2 or greater).

augur import beast [-h] --mcc MCC
                   [--most-recent-tip-date MOST_RECENT_TIP_DATE]
                   [--tip-date-regex TIP_DATE_REGEX]
                   [--tip-date-format TIP_DATE_FORMAT]
                   [--tip-date-delimeter TIP_DATE_DELIMETER] [--verbose]
                   [--recursion-limit RECURSION_LIMIT] --output-tree
                   OUTPUT_TREE --output-node-data OUTPUT_NODE_DATA

Named Arguments

--mcc

BEAST MCC tree

--most-recent-tip-date

Numeric date of most recent tip in tree (–tip-date-regex, –tip-date-format and –tip-date-delimeter are ignored if this is set)

Default: 0

--tip-date-regex

regex to extract dates from tip names

Default: '[0-9]{4}(\-[0-9]{2})*(\-[0-9]{2})*$'

--tip-date-format

Format of date (if extracted by regex)

Default: '%Y-%m-%d'

--tip-date-delimeter

delimeter used in tip-date-format. Used to match partial dates.

Default: '-'

--verbose

Display verbose output. Only useful for debugging.

Default: False

--recursion-limit

Set a custom recursion limit (dangerous!)

Default: False

--output-tree

file name to write tree to

--output-node-data

file name to write (temporal) branch lengths & BEAST traits as node data