oxbow.read_gtf

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oxbow.read_gtf#

oxbow.read_gtf(src, region=None, index=None, fields=None, attr_defs=None, compressed=False)#

Return Arrow IPC format from a GTF file.

Parameters:

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

  • region (str) – Genomic range string in the format “chr:start-end”, “chr:[start,end]” or “chr:[start,end)”.

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

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

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

Returns:

Arrow IPC

Return type:

bytes

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