Deprecatedļ
These features are deprecated, which means they are no longer maintained and will go away in a future major version of Augur. They are currently still available for backwards compatibility, but should not be used in new code.
augur parse
preference of name
over strain
as the sequence ID fieldļ
Deprecated in February 2024. Planned to be reordered June 2024 or after.
Currently, augur parse
checks for a ānameā field and then a āstrainā field to use as a sequence ID. This order will be changed in favor of searching for a āstrainā and then a ānameā field to be more consistent with the rest of Augur.
Users who have both ānameā and āstrainā fields in their data, and want to favor using the ānameā field should add the following augur parse
parameter --output-id-field 'name'
.
augur.utils.read_strains
ļ
Deprecated in December 2023. Planned for removal March 2024 or after.
This is part of a larger effort to formalize Augurās Python API.
We recognize the existing usage of this function, so it has been moved to
augur.io.read_strains
.
augur export v1
ļ
Deprecated in version 22.2.0 (July 2023). Planned for removal January 2024 or after.
augur export v2
was introduced in Augur version 6.0.0. Migrate by following
the official guide.
augur ancestral --output
ļ
Deprecated in version 5.2.0 (December 2019). Removed in version 7.0.0 (April 2020).
--output
was replaced by --output-node-data
to accommodate the addition of
--output-sequences
.