:py:mod:`pyranges.get_fasta`
============================

.. py:module:: pyranges.get_fasta


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


Functions
~~~~~~~~~

.. autoapisummary::

   pyranges.get_fasta.get_fasta



.. py:function:: get_fasta(gr, path=None, pyfaidx_fasta=None)

   Get fasta sequence.

   :param gr: Coordinates.
   :type gr: PyRanges
   :param path: Path to fasta file. It will be indexed using pyfaidx if an index is not found
   :type path: str
   :param pyfaidx_fasta: Alternative method to provide fasta target, as a pyfaidx.Fasta object
   :type pyfaidx_fasta: pyfaidx.Fasta

   :returns: Sequences, one per interval.
   :rtype: Series

   .. note::

      Sorting the PyRanges is likely to improve the speed.
      Intervals on the negative strand will be reverse complemented.

   .. warning:: Note that the names in the fasta header and gr must be the same.

   .. rubric:: Examples

   >>> gr = pr.from_dict({"Chromosome": ["chr1", "chr1"],
   ...                    "Start": [5, 0], "End": [8, 5]})

   >>> gr
   +--------------+-----------+-----------+
   | Chromosome   |     Start |       End |
   | (category)   |   (int32) |   (int32) |
   |--------------+-----------+-----------|
   | chr1         |         5 |         8 |
   | chr1         |         0 |         5 |
   +--------------+-----------+-----------+
   Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes.
   For printing, the PyRanges was sorted on Chromosome.

   >>> tmp_handle = open("temp.fasta", "w+")
   >>> _ = tmp_handle.write("> chr1\n")
   >>> _ = tmp_handle.write("ATTACCAT")
   >>> tmp_handle.close()

   >>> seq = pr.get_fasta(gr, "temp.fasta")

   >>> seq
   0      CAT
   1    ATTAC
   dtype: object

   >>> gr.seq = seq
   >>> gr
   +--------------+-----------+-----------+------------+
   | Chromosome   |     Start |       End | seq        |
   | (category)   |   (int32) |   (int32) | (object)   |
   |--------------+-----------+-----------+------------|
   | chr1         |         5 |         8 | CAT        |
   | chr1         |         0 |         5 | ATTAC      |
   +--------------+-----------+-----------+------------+
   Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes.
   For printing, the PyRanges was sorted on Chromosome.