oxbow.core.PyFastqScanner

oxbow.core.PyFastqScanner#

class oxbow.core.PyFastqScanner(src, compressed=False)#

A FASTQ file scanner.

Parameters:

  • src (str or file-like) – The path to the FASTQ file or a file-like object.

  • compressed (bool, optional [default: False]) – Whether the source is GZIP-compressed.

__init__()#

Methods

__init__()

field_names()

Return the names of the fixed fields.

scan([fields, batch_size, limit])

Scan the source as record batches.

scan_byte_ranges(byte_ranges[, fields, ...])

Scan batches of records from specified byte ranges in the file.

scan_virtual_ranges(vpos_ranges[, fields, ...])

Scan batches of records from virtual position ranges in a BGZF file.

schema([fields])

Return the Arrow schema.
field_names()#

Return the names of the fixed fields.

scan(fields=None, batch_size=1024, limit=None)#

Scan the source as record batches.

Parameters:

  • fields (list[str], optional) – Names of the fixed fields to project.

  • batch_size (int, optional [default: 1024]) – The number of records to include in each batch.

  • limit (int, optional) – The maximum number of records to scan. If None, records are scanned until EOF.

Returns:

An iterator yielding Arrow record batches.

Return type:

arro3 RecordBatchReader (pycapsule)

scan_byte_ranges(byte_ranges, fields=None, batch_size=1024, limit=None)#

Scan batches of records from specified byte ranges in the file.

The byte positions must align with record boundaries.

Parameters:

  • byte_ranges (list[tuple[int, int]]) – List of (start, end) byte position tuples to read from.

  • fields (list[str], optional) – Names of the fixed fields to project.

  • batch_size (int, optional [default: 1024]) – The number of records to include in each batch.

  • limit (int, optional) – The maximum number of records to scan. If None, all records in the specified ranges are scanned.

Returns:

An iterator yielding Arrow record batches.

Return type:

arro3 RecordBatchReader (pycapsule)

scan_virtual_ranges(vpos_ranges, fields=None, batch_size=1024, limit=None)#

Scan batches of records from virtual position ranges in a BGZF file.

The virtual positions must align with record boundaries. That means that the compressed offset must point to the beginning of a BGZF block and the uncompressed offset must point to the beginning or end of a record decoded within the block.

Parameters:

  • vpos_ranges (list[tuple[vpos, vpos]]) – List of virtual position ranges as pairs. Each virtual position can be given as either a packed virtual position (int), or an unpacked tuple of ints (c, u) specifying the compressed and uncompressed offsets, respectively.

  • fields (list[str], optional) – Names of the fixed fields to project.

  • batch_size (int, optional [default: 1024]) – The number of records to include in each batch.

  • limit (int, optional) – The maximum number of records to scan. If None, all records in the specified ranges are scanned.

Returns:

An iterator yielding Arrow record batches.

Return type:

arro3 RecordBatchReader (pycapsule)

schema(fields=None)#

Return the Arrow schema.

Parameters:

fields (list[str], optional) – Names of the fixed fields to project.

Return type:

arro3 Schema (pycapsule)

Contents