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.

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)

schema(fields=None)#

Return the Arrow schema.

Parameters:

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

Return type:

arro3 Schema (pycapsule)

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