agglovar.fa
===========

.. py:module:: agglovar.fa

.. autoapi-nested-parse::

   Reference and FASTA processing utilities.



Functions
---------

.. autoapisummary::

   agglovar.fa.fa_info
   agglovar.fa.read_fai


Module Contents
---------------

.. py:function:: fa_info(ref_fa: str | pathlib.Path) -> polars.DataFrame

   Get a table of reference information from a FASTA file.

   FASTA must have a ".fai".

   Table columns:
       chrom: Chromosome name.
       md5: MD5 of the sequence.
       order: Order of the sequence in the FASTA file.
       pos: Start position of the sequence in the FASTA file.
       line_bp: Number of base pairs per line.
       line_bytes: Number of bytes per line.

   :param ref_fa: Reference FASTA.

   :returns: A table with sequence information.


.. py:function:: read_fai(fai_file_name: str | pathlib.Path, cols: Optional[Iterable[str]] = ('chrom', 'len'), name: str = None) -> polars.DataFrame

   Read an FAI File name.

   By default, return a Series of chromosome lengths keyed by the chromosome (or contig) name.

   Available columns are: chrom, len, pos, line_bp, line_bytes

   :param fai_file_name: File to read.
   :param cols: Select these columns. None to retain all columns.
   :param name: Name of the chromosome column (typically "qry_id" to match query alignment tables).


   :returns: A table of the FAI file.