Cladetime¶
Cladetime is a Python interface for accessing past and present Nextstrain-produced SARS-CoV-2 sequence data, including sequence clade assignments. Cladetime can also “time travel” by using prior versions of reference trees to assign clades to sequences.
Installation¶
Cladetime can be installed with pip:
$ pip install cladetime
Detailed documentation¶
See the User Guide for more details about working with Cladetime.
The API Reference documentation provides API-level documentation.
Usage¶
Cladetime’s CladeTime class provides a lightweight wrapper around
historical and current SARS-CoV-2 GenBank sequence and sequence metadata
created by daily Nextstrain
workflows.
See the User Guide for examples of creating CladeTime objects that can access past sequence data and use past reference trees to assign clades to sequences.
>>> import polars as pl
>>> from cladetime import CladeTime, sequence
>>> ct = CladeTime()
>>> filtered_sequence_metadata = sequence.filter_metadata(
... ct.sequence_metadata
... )
>>> filtered_sequence_metadata.head(5).collect()
shape: (5, 6)
┌───────┬─────────┬────────────┬────────────────────────────┬──────────────┬──────────┐
│ clade ┆ country ┆ date ┆ strain ┆ host ┆ location │
│ --- ┆ --- ┆ --- ┆ --- ┆ --- ┆ --- │
│ str ┆ str ┆ date ┆ str ┆ str ┆ str │
╞═══════╪═════════╪════════════╪════════════════════════════╪══════════════╪══════════╡
│ 22A ┆ USA ┆ 2022-07-07 ┆ Alabama/SEARCH-202312/2022 ┆ Homo sapiens ┆ AL │
│ 22B ┆ USA ┆ 2022-07-02 ┆ Arizona/SEARCH-201153/2022 ┆ Homo sapiens ┆ AZ │
│ 22B ┆ USA ┆ 2022-07-19 ┆ Arizona/SEARCH-203528/2022 ┆ Homo sapiens ┆ AZ │
│ 22B ┆ USA ┆ 2022-07-15 ┆ Arizona/SEARCH-203621/2022 ┆ Homo sapiens ┆ AZ │
│ 22B ┆ USA ┆ 2022-07-20 ┆ Arizona/SEARCH-203625/2022 ┆ Homo sapiens ┆ AZ │
└───────┴─────────┴────────────┴────────────────────────────┴──────────────┴──────────┘