oxbow.core.PyCramScanner

class oxbow.core.PyCramScanner(src, compressed=None)

A CRAM file scanner.

Parameters:

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

__init__()

Methods

__init__()
chrom_names()	Return the names of the reference sequences.
chrom_sizes()	Return the names of the reference sequences and their lengths in bp.
field_names()	Return the names of the fixed fields.
scan([reference, reference_index, fields, ...])	Scan batches of records from the file.
scan_query(region[, index, reference, ...])	Scan batches of records from a genomic range.
schema([fields, tag_defs])	Return the Arrow schema.
tag_defs([scan_rows])	Discover tag definitions by sniffing scan_rows records.

chrom_names()

Return the names of the reference sequences.

chrom_sizes()

Return the names of the reference sequences and their lengths in bp.

field_names()

Return the names of the fixed fields.

scan(reference=None, reference_index=None, fields=None, tag_defs=None, batch_size=1024, limit=None)

Scan batches of records from the file.

Parameters:

• reference (path or file-like, optional) – The external reference FASTA file to use for decoding bases in the CRAM records. If not provided, sequence bases or references must be embedded in the CRAM file.

• reference_index (path or file-like, optional) – The index file for the reference FASTA file.

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

• tag_defs (list[tuple[str, str]], optional) – Definitions of tag 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_query(region, index=None, reference=None, reference_index=None, fields=None, tag_defs=None, batch_size=1024, limit=None)

Scan batches of records from a genomic range.

This operation requires an index 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. If None and the source was provided as a path, we will attempt to load the index from the same path with an additional extension.

• reference (path or file-like, optional) – The external reference FASTA file to use for decoding bases in the CRAM records. If not provided, sequence bases or references must be embedded in the CRAM file.

• reference_index (path or file-like, optional) – The index file for the reference FASTA file.

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

• tag_defs (list[tuple[str, str]], optional) – Definitions of tag 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 intersecting the query range are scanned.

Returns:

An iterator yielding Arrow record batches.

Return type:

arro3 RecordBatchReader (pycapsule)

schema(fields=None, tag_defs=None)

Return the Arrow schema.

Parameters:

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

• tag_defs (list[tuple[str, str]], optional) – Definitions of tag fields to project.

Return type:

arro3 Schema (pycapsule)

tag_defs(scan_rows=1024)

Discover tag 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.

Returns:

A list of tag definitions, where each definition is a tuple of the tag name and the SAM tag type code.

Return type:

list[tuple[str, str]]