bsxplorer.Genome.cds

Genome.cds(min_length: int = 100) → DataFrame[source]

Filter annotation by type == CDS and length threshold.

Warning

This method will have empty output, if type is not specified in input file.

Parameters:: min_length – Region length threshold.
Return type:: Return polars.DataFrame for downstream usage.

Examples

>>> path = "/path/to/genome.gff"
>>> genome = genome.from_gff(path)
>>> genome.cds(min_length=200)
shape: (81_837, 7)
┌─────────────┬────────┬────────┬────────┬──────────┬────────────┬─────────────────┐
│ chr         ┆ strand ┆ start  ┆ end    ┆ upstream ┆ downstream ┆ id              │
│ ---         ┆ ---    ┆ ---    ┆ ---    ┆ ---      ┆ ---        ┆ ---             │
│ str         ┆ str    ┆ u64    ┆ u64    ┆ u64      ┆ u64        ┆ str             │
╞═════════════╪════════╪════════╪════════╪══════════╪════════════╪═════════════════╡
│ NC_003070.9 ┆ +      ┆ 3996   ┆ 4276   ┆ 3996     ┆ 4276       ┆ cds-NP_171609.1 │
│ …           ┆ …      ┆ …      ┆ …      ┆ …        ┆ …          ┆ …               │
│ NC_000932.1 ┆ +      ┆ 152806 ┆ 153195 ┆ 152806   ┆ 153195     ┆ cds-NP_051123.1 │
│ NC_000932.1 ┆ +      ┆ 153878 ┆ 154312 ┆ 153878   ┆ 154312     ┆ cds-NP_051123.1 │
└─────────────┴────────┴────────┴────────┴──────────┴────────────┴─────────────────┘