modos.genomics.cram
===================

.. py:module:: modos.genomics.cram

.. autoapi-nested-parse::

   Utilities to interact with genomic intervals in CRAM files.



Classes
-------

.. autoapisummary::

   modos.genomics.cram.Region


Functions
---------

.. autoapisummary::

   modos.genomics.cram.extract_cram_metadata
   modos.genomics.cram.validate_cram_files
   modos.genomics.cram.create_sequence_id


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

.. py:class:: Region

   Genomic region consisting of a chromosome (aka reference) name
   and a 0-indexed half-open coordinate interval.
   Note that the end may not be specified, in which it will be set to math.inf.


   .. py:attribute:: chrom
      :type:  str


   .. py:attribute:: start
      :type:  int


   .. py:attribute:: end
      :type:  int | float


   .. py:method:: __post_init__()


   .. py:method:: to_htsget_query()

      Serializes the region into an htsget URL query.

      .. rubric:: Example

      >>> Region(chrom='chr1', start=0, end=100).to_htsget_query()
      'referenceName=chr1&start=0&end=100'



   .. py:method:: to_tuple()

      Return the region as a simple tuple.



   .. py:method:: from_htsget_query(url)
      :classmethod:


      Instantiate from an htsget URL query

      .. rubric:: Example

      >>> Region.from_htsget_query(
      ...   "http://localhost/htsget/reads/ex/demo1?format=CRAM&referenceName=chr1&start=0"
      ... )
      Region(chrom='chr1', start=0, end=inf)



   .. py:method:: from_ucsc(ucsc)
      :classmethod:


      Instantiate from a UCSC-formatted region string.

      .. rubric:: Example

      >>> Region.from_ucsc('chr-1ba:10-320')
      Region(chrom='chr-1ba', start=10, end=320)
      >>> Region.from_ucsc('chr1:-320')
      Region(chrom='chr1', start=0, end=320)
      >>> Region.from_ucsc('chr1:10-')
      Region(chrom='chr1', start=10, end=inf)
      >>> Region.from_ucsc('chr1:10')
      Region(chrom='chr1', start=10, end=inf)

      .. note::

         For more information about the UCSC coordinate system,
         see: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms



   .. py:method:: from_pysam(record)
      :classmethod:



   .. py:method:: overlaps(other)

      Checks if other in self.
      This check if any portion of other overlaps with self.



   .. py:method:: contains(other)

      Checks if other is fully contained in self.



.. py:function:: extract_cram_metadata(cram)

   Extract metadata from the CRAM file header and
   convert specific attributes according to the modo schema.


.. py:function:: validate_cram_files(cram_path)

   Validate CRAM files using pysam.
   Checks if the file is sorted and has an index.


.. py:function:: create_sequence_id(name, sequence_md5)

   Helper function to create a unique id from a sequence name and md5 hash