Metadata-Version: 2.1
Name: pyjaspar
Version: 2.1.0
Summary: A serverless interface to Biopython to access different versions of JASPAR database
Home-page: https://github.com/asntech/pyjaspar
Author: Aziz Khan
Author-email: azez.khan@gmail.com
License: GPL
Description: pyJASPAR
        --------
        
            A Pythonic interface to JASPAR transcription factor motifs
        
        **pyJASPAR** uses *Biopython* and *SQLite3* to provide a serverless interface to `JASPAR database <http://jaspar.genereg.net>`_ to query and access TF motif profiles across various releases of JASPAR.
        
        
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4509415.svg
           :target: https://doi.org/10.5281/zenodo.4509415
        
        .. image:: https://travis-ci.org/asntech/pyjaspar.svg?branch=main
            :target: https://travis-ci.org/asntech/pyjaspar
        
        .. image:: https://img.shields.io/pypi/pyversions/pyjaspar.svg
            :target: https://www.python.org
        
        .. image:: https://img.shields.io/pypi/v/pyjaspar.svg
            :target: https://pypi.python.org/pypi/pyjaspar
        
        .. image:: https://anaconda.org/bioconda/pyjaspar/badges/version.svg
            :target: https://anaconda.org/bioconda/pyjaspar
        
        .. image:: https://anaconda.org/bioconda/pyjaspar/badges/downloads.svg
            :target: https://bioconda.github.io/recipes/pyjaspar/README.html
        
        .. image:: https://img.shields.io/github/issues/asntech/pyjaspar.svg
            :target: https://github.com/asntech/pyjaspar/issues
        
        
        pyJASPAR provides access to the following releases of JASPAR database:
            - `JASPAR2022 <http://jaspar.genereg.net>`_
            - `JASPAR2020 <http://jaspar2020.genereg.net>`_
            - `JASPAR2018 <http://jaspar2018.genereg.net>`_
            - `JASPAR2016 <http://jaspar2016.genereg.net>`_
            - `JASPAR2014 <http://jaspar2014.genereg.net>`_
        
        
        **Note**: This is a serverless SQLite wrapper around the Biopython JASPAR module `Bio.motifs.jaspar.db` which requires JASPAR MySQL database sever connection details.
        
        
        Documentation
        -------------
        
        **A detailed documentation is available in different formats:**  `HTML <http://pyjaspar.readthedocs.org>`_ | `PDF <http://readthedocs.org/projects/pyjaspar/downloads/pdf/latest/>`_ | `ePUB <http://readthedocs.org/projects/pyjaspar/downloads/epub/latest/>`_
        
        
        Installation
        ------------
        
        Quick installation using conda
        ================================
        pyJASPAR is available on `Bioconda <https://anaconda.org/bioconda/pyjaspar>`_ for installation via ``conda``.
        
        .. code-block:: bash
        
        	conda install -c bioconda pyjaspar
        
        
        Install using pip
        ==================
        pyJASPAR is also available on `PyPi <https://pypi.org/project/pyjaspar/>`_ for installation via ``pip``.
        
        .. code-block:: bash
        
        	pip install pyjaspar
        	
        
        pyJASPAR uses BioPython and it supports python ``3.x``. 
        
        Install pyjaspar from source
        =============================
        You can install a development version by using ``git`` from GitHub.
        
        
        Install development version from `GitHub`
        ==========================================
        If you have `git` installed, use this:
        
        .. code-block:: bash
        
            git clone https://github.com/asntech/pyjaspar.git
            cd pyjaspar
            python setup.py sdist install
        
        How to use pyJASPAR?
        --------------------
        
        Once you have installed pyjaspar, you can create jaspardb class object:
        
        .. code-block:: pycon
        
            >>> from pyjaspar import jaspardb
            
            #Create the JASPAR2020 release object    
            >>> jdb_obj = jaspardb(release='JASPAR2020')
        
            #Fetch motif by ID
            >>> motif = jdb_obj.fetch_motif_by_id('MA0095.2')
            >>> print(motif.name)
            YY1
        
            #Fetch motifs by TF name
            >>> motifs = jdb_obj.fetch_motifs_by_name('CTCF')
            >>> print(len(motifs))
            2
        
            #Get CORE vertebrates collection
            >>> motifs = jdb_obj.fetch_motifs(
                collection = 'CORE',
                tax_group = ['vertebrates']
                )
            >>> print(len(motifs))
            746
            ## loop through the motifs list and perform analysis
            >>> for motif in motifs:
                    pass
        
        **Note**: Above methods return `Bio.motifs.jaspar.Motif` object. You can find more details `here <http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec262>`_ 
        
        
        Find available releases
        =======================
        .. code-block:: pycon
            
            >>> print(jdb_obj.get_releases())
            ['JASPAR2022','JASPAR2020', 'JASPAR2018', 'JASPAR2016', 'JASPAR2014']
        
        
        Cite
        =====
            - Aziz Khan. pyJASPAR: a Pythonic interface to JASPAR transcription factor motifs. (2021). doi:10.5281/zenodo.4509415
        
        .. code-block:: bash
        
            @software{aziz_khan_2021_4509415,
              author       = {Aziz Khan},
              title        = {{pyJASPAR: a Pythonic interface to JASPAR transcription factor motifs}},
              month        = feb,
              year         = 2021,
              publisher    = {Zenodo},
              version      = {v2.0.0},
              doi          = {10.5281/zenodo.4509415},
              url          = {https://doi.org/10.5281/zenodo.4509415}
            }
        
Platform: linux/unix
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/x-rst
