modos.genomics.formats
======================

.. py:module:: modos.genomics.formats


Classes
-------

.. autoapisummary::

   modos.genomics.formats.Region
   modos.genomics.formats.GenomicFileSuffix


Functions
---------

.. autoapisummary::

   modos.genomics.formats.read_pysam


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:class:: GenomicFileSuffix

   Bases: :py:obj:`tuple`, :py:obj:`enum.Enum`


   Enumeration of all supported genomic file suffixes.


   .. py:attribute:: CRAM
      :value: ('.cram',)



   .. py:attribute:: BAM
      :value: ('.bam',)



   .. py:attribute:: SAM
      :value: ('.sam',)



   .. py:attribute:: VCF
      :value: ('.vcf', '.vcf.gz')



   .. py:attribute:: BCF
      :value: ('.bcf',)



   .. py:attribute:: FASTA
      :value: ('.fasta', '.fa')



   .. py:attribute:: FASTQ
      :value: ('.fastq', '.fq')



   .. py:method:: from_path(path)
      :classmethod:



   .. py:method:: get_index_suffix()

      Return the supported index suffix related to a genomic filetype



   .. py:method:: to_htsget_endpoint()

      Return the htsget endpoint for a genomic file type



.. py:function:: read_pysam(path, region = None, **kwargs)

   Automatically instantiate a pysam file object from input path and passes any additional kwarg to it.