oxbow.core.PyGffScanner

oxbow.core.PyGffScanner#

class oxbow.core.PyGffScanner(src, compressed=False, fields=None, attribute_defs=None)#

A GFF file scanner.

Parameters:

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

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

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

  • attribute_defs (list[tuple[str, str]], optional [default: None]) – Definitions for the "attributes" struct column. None omits the attributes column. Use the attribute_defs() method to discover definitions.

__init__()#

Methods

__init__()

attribute_defs([scan_rows])

Discover attribute definitions by sniffing scan_rows records.

field_names()

Return the names of the fixed fields.

scan([columns, batch_size, limit])

Scan batches of records from the file.

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

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

scan_query(region[, index, columns, ...])

Scan batches of records from a genomic range query on a BGZF-encoded file.

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

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

schema()

Return the Arrow schema.
attribute_defs(scan_rows=1024)#

Discover attribute definitions by sniffing scan_rows records.

The reader stream is reset to its original position after scanning.

Parameters:

scan_rows (int, optional [default: 1024]) – The number of records to scan. If None, all records are scanned.

Returns:

A list of attribute definitions, where each definition is a tuple of the attribute name and its type (String or Array).

Return type:

list[tuple[str, str]]

field_names()#

Return the names of the fixed fields.

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

Scan batches of records from the file.

Parameters:

  • columns (list[str], optional) – Names of the columns 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.

Return type:

arro3 RecordBatchReader (pycapsule)

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

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

Parameters:

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

  • columns (list[str], optional) – Names of the columns 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.

Return type:

arro3 RecordBatchReader (pycapsule)

scan_query(region, index=None, columns=None, batch_size=1024, limit=None)#

Scan batches of records from a genomic range query on a BGZF-encoded file.

Parameters:

  • region (str) – Genomic region in the format “chr:start-end”.

  • index (path or file-like, optional) – The index file to use for querying the region.

  • columns (list[str], optional) – Names of the columns 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.

Return type:

arro3 RecordBatchReader (pycapsule)

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

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

Parameters:

  • vpos_ranges (list[tuple[vpos, vpos]]) – List of virtual position ranges as pairs.

  • columns (list[str], optional) – Names of the columns 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.

Return type:

arro3 RecordBatchReader (pycapsule)

schema()#

Return the Arrow schema.

Return type:

arro3 Schema (pycapsule)

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