oxbow.read_fasta

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oxbow.read_fasta#

oxbow.read_fasta(src, regions=None, index=None, gzi=None, fields=None, compressed=False)#

Return Arrow IPC format from a FASTA file.

Parameters:

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

  • regions (list[str], optional) – Genomic ranges in the format “chr:start-end”, “chr:[start,end]” or “chr:[start,end)”.

  • index (path or file-like, optional) – The FAI index file.

  • gzi (path or file-like, optional) – A GZI index file for BGZF-encoded sources.

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

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

Returns:

Arrow IPC

Return type:

bytes

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