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immunum.polars

immunum.polars.number(expr, *, chains, scheme, min_confidence=None)

Segment a polars expr with immunum.

Annotator object will be initialized with chains, scheme, min_confidence. Results are returned as Struct({'chain': String, 'scheme': String, 'positions': List(String), 'residues': List(String)})

Example:

import polars as pl
import immunum.polars as imp

df = pl.DataFrame(
    {
        "sequence": [
            "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS",
            "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK",
        ]
    }
).select(
    imp.number(
        "sequence",
        chains=["h"],
        scheme="imgt",
        min_confidence=0.0,
    ).alias("numbering")
)
assert df.dtypes == [
    pl.Struct(
        {
            "chain": pl.String,
            "scheme": pl.String,
            "positions": pl.List(
                pl.String
            ),
            "residues": pl.List(
                pl.String
            ),
        }
    )
]
print(
    df.select(
        pl.col(
            "numbering"
        ).struct.unnest()
    )
)

# shape: (2, 4)
# ┌───────┬────────┬─────────────────────┬───────────────────┐
# │ chain ┆ scheme ┆ positions           ┆ residues          │
# │ ---   ┆ ---    ┆ ---                 ┆ ---               │
# │ str   ┆ str    ┆ list[str]           ┆ list[str]         │
# ╞═══════╪════════╪═════════════════════╪═══════════════════╡
# │ H     ┆ IMGT   ┆ ["1", "2", … "128"] ┆ ["Q", "V", … "S"] │
# │ H     ┆ IMGT   ┆ ["1", "2", … "127"] ┆ ["D", "I", … "K"] │
# └───────┴────────┴─────────────────────┴───────────────────┘

Parameters:

Name Type Description Default
expr IntoExprColumn

input polars expression (e.g. pl.col('sequence'))

 required
chains list[str]

list of chains to use for initialized Annotator

 required
scheme str

scheme to use for initialized Annotator

 required
min_confidence float | None

confidence to use for initialized Annotator. Defaults to None (corresponds to 0.5)

 None

Returns:

Type Description
Expr

pl.Expr: numbering expression
Source code in immunum/polars.py 
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def number(
    expr: IntoExprColumn,
    *,
    chains: list[str],
    scheme: str,
    min_confidence: float | None = None,
) -> pl.Expr:
    """Segment a polars expr with immunum.

    Annotator object will be initialized with chains, scheme, min_confidence.
    Results are returned as `Struct({'chain': String, 'scheme': String, 'positions': List(String), 'residues': List(String)})`

    Example:

    ```python
    import polars as pl
    import immunum.polars as imp

    df = pl.DataFrame(
        {
            "sequence": [
                "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS",
                "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK",
            ]
        }
    ).select(
        imp.number(
            "sequence",
            chains=["h"],
            scheme="imgt",
            min_confidence=0.0,
        ).alias("numbering")
    )
    assert df.dtypes == [
        pl.Struct(
            {
                "chain": pl.String,
                "scheme": pl.String,
                "positions": pl.List(
                    pl.String
                ),
                "residues": pl.List(
                    pl.String
                ),
            }
        )
    ]
    print(
        df.select(
            pl.col(
                "numbering"
            ).struct.unnest()
        )
    )

    # shape: (2, 4)
    # ┌───────┬────────┬─────────────────────┬───────────────────┐
    # │ chain ┆ scheme ┆ positions           ┆ residues          │
    # │ ---   ┆ ---    ┆ ---                 ┆ ---               │
    # │ str   ┆ str    ┆ list[str]           ┆ list[str]         │
    # ╞═══════╪════════╪═════════════════════╪═══════════════════╡
    # │ H     ┆ IMGT   ┆ ["1", "2", … "128"] ┆ ["Q", "V", … "S"] │
    # │ H     ┆ IMGT   ┆ ["1", "2", … "127"] ┆ ["D", "I", … "K"] │
    # └───────┴────────┴─────────────────────┴───────────────────┘
    ```

    Args:
        expr (IntoExprColumn): input polars expression (e.g. `pl.col('sequence')`)
        chains (list[str]): list of chains to use for initialized `Annotator`
        scheme (str): scheme to use for initialized `Annotator`
        min_confidence (float | None, optional): confidence to use for initialized `Annotator`. Defaults to None (corresponds to 0.5)

    Returns:
        pl.Expr: numbering expression
    """
    return register_plugin_function(
        args=[expr],
        plugin_path=LIB,
        function_name="numbering_struct_expr",
        is_elementwise=True,
        kwargs={
            "chains": _normalize_chains(chains),
            "scheme": _normalize_scheme(scheme),
            "min_confidence": min_confidence,
        },
    )

immunum.polars.segment(expr, *, chains, scheme, min_confidence=None)

Split sequences into FR/CDR regions as a Polars expression.

Annotator object will be initialized with chains, scheme, min_confidence. Results are returned as Struct({'fr1': String, 'cdr1': String, 'fr2': String, 'cdr2': String, 'fr3': String, 'cdr3': String, 'fr4': String, 'prefix': String, 'postfix': String}).

Example:

import polars as pl
import immunum.polars as imp

df = pl.DataFrame(
    {
        "sequence": [
            "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS",
            "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK",
        ]
    }
).select(
    imp.segment(
        "sequence",
        chains=["h", "k", "l"],
        scheme="imgt",
        min_confidence=0.0,
    ).alias("segmentation")
)
assert df[
    "segmentation"
].dtype == pl.Struct(
    {
        "prefix": pl.String,
        "fr1": pl.String,
        "cdr1": pl.String,
        "fr2": pl.String,
        "cdr2": pl.String,
        "fr3": pl.String,
        "cdr3": pl.String,
        "fr4": pl.String,
        "postfix": pl.String,
    }
)
print(
    df.select(
        pl.col(
            "segmentation"
        ).struct.unnest()
    )
)

# shape: (2, 9)
# ┌────────────────────────┬──────────┬───┬─────────────┬────────┬─────────┐
# │ fr1                    ┆ cdr1     ┆ … ┆ fr4         ┆ prefix ┆ postfix │
# │ ---                    ┆ ---      ┆   ┆ ---         ┆ ---    ┆ ---     │
# │ str                    ┆ str      ┆   ┆ str         ┆ str    ┆ str     │
# ╞════════════════════════╪══════════╪═══╪═════════════╪════════╪═════════╡
# │ QVQLVQSGAEVKRPGSSVTVS… ┆ GGSFSTYA ┆ … ┆ WGQGTLVTVSS ┆        ┆         │
# │ DIQMTQSPSSLSASVGDRVTI… ┆ RASQDVNT ┆ … ┆ FGQGTKVEIK  ┆        ┆         │
# └────────────────────────┴──────────┴───┴─────────────┴────────┴─────────┘

Parameters:

Name Type Description Default
expr IntoExprColumn

input polars expression (e.g. pl.col('sequence'))

 required
chains list[str]

list of chains to use for initialized Annotator

 required
scheme str

scheme to use for initialized Annotator

 required
min_confidence float | None

confidence to use for initialized Annotator. Defaults to None (corresponds to 0.5)

 None

Returns:

Type Description
Expr

pl.Expr: segmentation expression
Source code in immunum/polars.py 
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def segment(
    expr: IntoExprColumn,
    *,
    chains: list[str],
    scheme: str,
    min_confidence: float | None = None,
) -> pl.Expr:
    """Split sequences into FR/CDR regions as a Polars expression.

    Annotator object will be initialized with chains, scheme, min_confidence.
    Results are returned as `Struct({'fr1': String, 'cdr1': String, 'fr2': String, 'cdr2': String, 'fr3': String, 'cdr3': String, 'fr4': String, 'prefix': String, 'postfix': String})`.

    Example:

    ```python
    import polars as pl
    import immunum.polars as imp

    df = pl.DataFrame(
        {
            "sequence": [
                "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS",
                "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK",
            ]
        }
    ).select(
        imp.segment(
            "sequence",
            chains=["h", "k", "l"],
            scheme="imgt",
            min_confidence=0.0,
        ).alias("segmentation")
    )
    assert df[
        "segmentation"
    ].dtype == pl.Struct(
        {
            "prefix": pl.String,
            "fr1": pl.String,
            "cdr1": pl.String,
            "fr2": pl.String,
            "cdr2": pl.String,
            "fr3": pl.String,
            "cdr3": pl.String,
            "fr4": pl.String,
            "postfix": pl.String,
        }
    )
    print(
        df.select(
            pl.col(
                "segmentation"
            ).struct.unnest()
        )
    )

    # shape: (2, 9)
    # ┌────────────────────────┬──────────┬───┬─────────────┬────────┬─────────┐
    # │ fr1                    ┆ cdr1     ┆ … ┆ fr4         ┆ prefix ┆ postfix │
    # │ ---                    ┆ ---      ┆   ┆ ---         ┆ ---    ┆ ---     │
    # │ str                    ┆ str      ┆   ┆ str         ┆ str    ┆ str     │
    # ╞════════════════════════╪══════════╪═══╪═════════════╪════════╪═════════╡
    # │ QVQLVQSGAEVKRPGSSVTVS… ┆ GGSFSTYA ┆ … ┆ WGQGTLVTVSS ┆        ┆         │
    # │ DIQMTQSPSSLSASVGDRVTI… ┆ RASQDVNT ┆ … ┆ FGQGTKVEIK  ┆        ┆         │
    # └────────────────────────┴──────────┴───┴─────────────┴────────┴─────────┘
    ```

    Args:
        expr (IntoExprColumn): input polars expression (e.g. `pl.col('sequence')`)
        chains (list[str]): list of chains to use for initialized `Annotator`
        scheme (str): scheme to use for initialized `Annotator`
        min_confidence (float | None, optional): confidence to use for initialized `Annotator`. Defaults to None (corresponds to 0.5)

    Returns:
        pl.Expr: segmentation expression
    """
    return register_plugin_function(
        args=[expr],
        plugin_path=LIB,
        function_name="segmentation_struct_expr",
        is_elementwise=True,
        kwargs={
            "chains": _normalize_chains(chains),
            "scheme": _normalize_scheme(scheme),
            "min_confidence": min_confidence,
        },
    )

immunum.polars.numbering_method(expr, *, annotator)

Number sequences using a pre-built Annotator instance.

Prefer this over number when reusing the same annotator across multiple expressions, as it avoids re-initializing the annotator on each call. Returns the same struct shape as number.

Example:

import polars as pl
import immunum
import immunum.polars as imp

annotator = immunum.Annotator(
    chains=["H", "K", "L"],
    scheme="imgt",
)

df = pl.DataFrame(
    {
        "sequence": [
            "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS",
        ]
    }
).select(
    imp.numbering_method(
        pl.col("sequence"),
        annotator=annotator,
    ).alias("numbering")
)
assert set(
    df["numbering"].struct.fields
) == {
    "chain",
    "scheme",
    "confidence",
    "numbering",
}

Parameters:

Name Type Description Default
expr IntoExprColumn

input polars expression (e.g. pl.col('sequence'))

 required
annotator Annotator

pre-built Annotator instance

 required

Returns:

Type Description
Expr

pl.Expr: numbering expression
Source code in immunum/polars.py 
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def numbering_method(expr: IntoExprColumn, *, annotator: Annotator) -> pl.Expr:
    """Number sequences using a pre-built `Annotator` instance.

    Prefer this over `number` when reusing the same annotator across multiple expressions,
    as it avoids re-initializing the annotator on each call. Returns the same struct shape
    as `number`.

    Example:

    ```python
    import polars as pl
    import immunum
    import immunum.polars as imp

    annotator = immunum.Annotator(
        chains=["H", "K", "L"],
        scheme="imgt",
    )

    df = pl.DataFrame(
        {
            "sequence": [
                "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS",
            ]
        }
    ).select(
        imp.numbering_method(
            pl.col("sequence"),
            annotator=annotator,
        ).alias("numbering")
    )
    assert set(
        df["numbering"].struct.fields
    ) == {
        "chain",
        "scheme",
        "confidence",
        "numbering",
    }
    ```

    Args:
        expr (IntoExprColumn): input polars expression (e.g. `pl.col('sequence')`)
        annotator (Annotator): pre-built `Annotator` instance

    Returns:
        pl.Expr: numbering expression
    """
    return register_plugin_function(
        args=[expr],
        plugin_path=LIB,
        function_name="numbering_class_struct_expr",
        is_elementwise=True,
        kwargs={"annotator": annotator._annotator},
    )

immunum.polars.segmentation_method(expr, *, annotator)

Segment sequences using a pre-built Annotator instance.

Prefer this over segment when reusing the same annotator across multiple expressions, as it avoids re-initializing the annotator on each call. Returns the same struct shape as segment.

Example:

import polars as pl
import immunum
import immunum.polars as imp

annotator = immunum.Annotator(
    chains=["H", "K", "L"],
    scheme="imgt",
)

df = pl.DataFrame(
    {
        "sequence": [
            "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS",
            "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK",
        ]
    }
).select(
    imp.segmentation_method(
        "sequence", annotator=annotator
    ).alias("segmentation")
)
assert df[
    "segmentation"
].dtype == pl.Struct(
    {
        "prefix": pl.String,
        "fr1": pl.String,
        "cdr1": pl.String,
        "fr2": pl.String,
        "cdr2": pl.String,
        "fr3": pl.String,
        "cdr3": pl.String,
        "fr4": pl.String,
        "postfix": pl.String,
    }
)

Parameters:

Name Type Description Default
expr IntoExprColumn

input polars expression (e.g. pl.col('sequence'))

 required
annotator Annotator

pre-built Annotator instance

 required

Returns:

Type Description
Expr

pl.Expr: segmentation expression
Source code in immunum/polars.py 
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def segmentation_method(expr: IntoExprColumn, *, annotator: Annotator) -> pl.Expr:
    """Segment sequences using a pre-built `Annotator` instance.

    Prefer this over `segment` when reusing the same annotator across multiple expressions,
    as it avoids re-initializing the annotator on each call. Returns the same struct shape
    as `segment`.

    Example:

    ```python
    import polars as pl
    import immunum
    import immunum.polars as imp

    annotator = immunum.Annotator(
        chains=["H", "K", "L"],
        scheme="imgt",
    )

    df = pl.DataFrame(
        {
            "sequence": [
                "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS",
                "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK",
            ]
        }
    ).select(
        imp.segmentation_method(
            "sequence", annotator=annotator
        ).alias("segmentation")
    )
    assert df[
        "segmentation"
    ].dtype == pl.Struct(
        {
            "prefix": pl.String,
            "fr1": pl.String,
            "cdr1": pl.String,
            "fr2": pl.String,
            "cdr2": pl.String,
            "fr3": pl.String,
            "cdr3": pl.String,
            "fr4": pl.String,
            "postfix": pl.String,
        }
    )
    ```

    Args:
        expr (IntoExprColumn): input polars expression (e.g. `pl.col('sequence')`)
        annotator (Annotator): pre-built `Annotator` instance

    Returns:
        pl.Expr: segmentation expression
    """
    return register_plugin_function(
        args=[expr],
        plugin_path=LIB,
        function_name="segmentation_class_struct_expr",
        is_elementwise=True,
        kwargs={"annotator": annotator._annotator},
    )