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API Reference

vcf_reader​

VCF File Readers.

VCFReader​

class VCFReader(Reader)

A VCF File Reader.

This class is used to read a VCF file and convert it to a polars DataFrame.

__init__​
def __init__(path: os.PathLike)

Initialize the VCFReader.

Arguments:

  • path Path - Path to the VCF file.
inner​
@property
def inner()

Return the inner reader.

VCFIndexedReader​

class VCFIndexedReader(Reader)

An Indexed VCF File Reader.

This class is used to read or query an indexed VCF file and convert it to a polars DataFrame.

__init__​
def __init__(path: os.PathLike)

Initialize the VCFIndexedReader.

inner​
@property
def inner()

Return the inner reader.

query​
def query(region: str) -> pa.RecordBatchReader

Query the VCF file and return a pyarrow RecordBatchReader.

Arguments:

  • region str - The region to query.

genbank_reader​

Genbank file reader.

GenbankReader​

class GenbankReader(Reader)

Genbank file reader.

__init__​
def __init__(path: os.PathLike,
             compression: Compression = Compression.INFERRED)

Read a genbank file.

Arguments:

  • path Path - Path to the fasta file.
  • compression Compression - Compression type of the file.
inner​
@property
def inner()

Return the inner reader.

mzml_reader​

MzML File Reader.

MzMLReader​

class MzMLReader(Reader)

A MzML File Reader.

__init__​
def __init__(path: os.PathLike,
             compression: Compression = Compression.INFERRED)

Initialize the MzMLReader.

Arguments:

  • path - The path to the MzML file.
inner​
@property
def inner()

Return the inner reader.

gtf_reader​

GTF File Reader.

GTFReader​

class GTFReader(Reader)

A GTF File Reader.

__init__​
def __init__(path: os.PathLike,
             compression: Compression = Compression.INFERRED)

Initialize the GTFReader.

Arguments:

  • path - The path to the GTF file.
to_polars​
def to_polars()

Read the GTF file and return a polars DataFrame.

to_arrow​
def to_arrow() -> pa.RecordBatchReader

Convert the GTF reader to an arrow batch reader.

to_arrow_scanner​
def to_arrow_scanner() -> ds.Scanner

Convert the GTF reader to an arrow scanner.

inner​
@property
def inner()

Return the inner reader.

fasta_reader​

FASTA file reader.

FastaReader​

class FastaReader(Reader)

FASTA file reader.

__init__​
def __init__(path: os.PathLike,
             compression: Compression = Compression.INFERRED)

Read a fasta file.

Arguments:

  • path Path - Path to the fasta file.

    Kwargs:

  • compression Compression - Compression type of the file. Defaults to Compression.INFERRED.

inner​
@property
def inner()

Return the inner reader.

compression​

Compression configuration.

Compression​

class Compression(Enum)

Compression types for files.

from_file​
@classmethod
def from_file(cls, path: os.PathLike) -> "Compression"

Infer the compression type from the file extension.

infer_or_use​
def infer_or_use(path: os.PathLike) -> "Compression"

Infer the compression type from the file extension if needed.

session​

__init__​

Main biobear package.

reader​

Abstract Reader class for reading data from a file or stream.

Reader​

class Reader(ABC)

An abstract base class (ABC) representing a reader.

The class defines basic functionalities for conversion, but the specifics must be implemented in a subclass.

inner​
@property
@abstractmethod
def inner()

Abstract property for the inner reader.

Returns:

The inner reader. The type of the reader is defined by the specific subclass.

to_pandas​
def to_pandas()

Convert the inner data to a Pandas DataFrame.

Returns:

  • pd.DataFrame - The converted data in a Pandas DataFrame.

Raises:

  • ImportError - If the 'pandas' package is not installed.
to_polars​
def to_polars()

Convert the inner data to a Polars DataFrame.

This method first converts the inner reader's data to an Arrow table, then to a Python dictionary, and finally to a Polars DataFrame.

Returns:

  • pl.DataFrame - The converted data in a Polars DataFrame.

Raises:

  • ImportError - If the 'polars' package is not installed.
to_arrow_scanner​
def to_arrow_scanner() -> ds.Scanner

Convert the inner data to an Arrow scanner.

This method first converts the inner reader's data to Arrow batches, and then forms a scanner from these batches.

Returns:

  • ds.Scanner - The converted data in an Arrow scanner.
to_arrow​
def to_arrow() -> pa.RecordBatchReader

Convert the inner data to an Arrow record batch reader.

If the inner reader is exhausted, this method raises an exception. Otherwise, it converts the inner reader's data to an Arrow record batch.

Returns:

  • pa.RecordBatchReader - The converted data in an Arrow record batch reader.

Raises:

  • StopIteration - If the inner reader is exhausted.

bam_reader​

BAM File Readers.

BamReader​

class BamReader(Reader)

A BAM File Reader.

__init__​
def __init__(path: os.PathLike)

Initialize the BamReader.

Arguments:

  • path Path - Path to the BAM file.
inner​
@property
def inner()

Return the inner reader.

BamIndexedReader​

class BamIndexedReader(Reader)

An Indexed BAM File Reader.

__init__​
def __init__(path: os.PathLike)

Initialize the BamIndexedReader.

Arguments:

  • path Path - Path to the BAM file.
  • index Path - Path to the BAM index file.
inner​
@property
def inner()

Return the inner reader.

query​
def query(region: str) -> pa.RecordBatchReader

Query the BAM file and return an Arrow RecordBatchReader.

Arguments:

  • region - A region in the format "chr:start-end".

fastq_reader​

FASTQ reader.

FastqReader​

class FastqReader(Reader)

FASTQ file reader.

__init__​
def __init__(path: os.PathLike,
             compression: Compression = Compression.INFERRED)

Read a fastq file.

Arguments:

  • path Path - Path to the fastq file.

    Kwargs:

  • compression Compression - Compression type of the file. Defaults to Compression.INFERRED.

inner​
@property
def inner()

Return the inner reader.

bcf_reader​

BCF File Readers.

BCFReader​

class BCFReader(Reader)

A BCF File Reader.

This class is used to read a BCF file and convert it to a polars DataFrame.

__init__​
def __init__(path: os.PathLike)

Initialize the BCFReader.

Arguments:

  • path Path - Path to the BCF file.
inner​
@property
def inner()

Return the inner reader.

BCFIndexedReader​

class BCFIndexedReader(Reader)

An Indexed BCF File Reader.

This class is used to read or query an indexed BCF file and convert it to a polars DataFrame.

__init__​
def __init__(path: os.PathLike)

Initialize the BCFIndexedReader.

inner​
@property
def inner()

Return the inner reader.

query​
def query(region: str) -> pa.RecordBatchReader

Query the BCF file and return an arrow batch reader.

Arguments:

  • region str - The region to query.

gff_reader​

GFF File Reader.

GFFReader​

class GFFReader(Reader)

A GFF File Reader.

__init__​
def __init__(path: os.PathLike,
             compression: Compression = Compression.INFERRED)

Initialize the GFFReader.

Arguments:

  • path - The path to the GFF file.
to_polars​
def to_polars()

Read the GFF file and return a polars DataFrame.

to_arrow​
def to_arrow() -> pa.RecordBatchReader

Convert the GFF reader to an arrow batch reader.

to_arrow_scanner​
def to_arrow_scanner() -> ds.Scanner

Convert the GFF reader to an arrow scanner.

inner​
@property
def inner()

Return the inner reader.