Metadata-Version: 2.1
Name: hybkit
Version: 0.2.0
Summary: Toolkit for analysis of .hyb format genomic sequence data from ribonomics experiments.
Home-page: https://github.com/RenneLab/hybkit
Author: Daniel Stribling
Author-email: ds@ufl.edu
License: UNKNOWN
Project-URL: Download as TAR, https://github.com/RenneLab/hybkit/tarball/0.2.0
Project-URL: Renne Lab Github, https://github.com/RenneLab
Project-URL: Renne Lab Mainpage, https://www.rennelab.com/
Project-URL: Hyb Format Specification, https://www.sciencedirect.com/science/article/pii/S1046202313004180
Description: 
        hybkit
        ==================================
        .. image:: https://img.shields.io/github/v/release/RenneLab/hybkit?include_prereleases
           :target: https://github.com/RenneLab/hybkit/releases
           :alt: GitHub release (latest by date including pre-releases)
        .. image:: https://badge.fury.io/py/hybkit.svg
           :target: https://pypi.org/project/hybkit/
           :alt: PyPI Package Version
        .. image:: https://readthedocs.org/projects/hybkit/badge/?version=latest
           :target: https://hybkit.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        .. image:: https://img.shields.io/pypi/pyversions/hybkit
           :target: https://pypi.org/project/hybkit/
           :alt: PyPI - Python Version
        
        
        | Welcome to *hybkit*, a toolkit for analysis of ".hyb" format genomic sequence data 
          generated from ribonomics techniques such as CLASH and qCLASH. 
        | This software is available via Github, at http://www.github.com/RenneLab/hybkit .
        | Full project documentation is available at
          `hybkit's ReadTheDocs <https://hybkit.readthedocs.io/>`_.
        
        This project contains multiple components:
            #. The hybkit toolkit of command-line utilities for manipulating,
               analyzing, and plotting data contained within hyb-format files.
            #. Analysis pipelines utilizing the toolkit for analysis of qCLASH hybrid sequence data.
            #. The hybkit python API, an extendable documented codebase
               for creation of custom analyses of hyb-format data.
        
        Hybkit Toolkit:
            hybkit includes command-line utilities for the manipulation of ".hyb" format data:
        
                =================================== =========================================================
                Utility                             Description
                =================================== =========================================================
                hyb_check                           Read a ".hyb" file and check for errors
                hyb_analyze                         Analyze and set details for hyb records, such as segtypes
                hyb_filter                          Filter a ".hyb" file to a specific subset of sequences
                hyb_type_analysis (pending)         Perform a type analysis on a prepared "hyb" file
                hyb_mirna_count_anlaysis (pending)  Perform a miRNA_count analysis on a prepared "hyb" file
                hyb_summary_anlaysis (pending)      Perform a summary analysis on a prepared "hyb" file
                hyb_mirna_target_analysis (pending) Perform a mirna_target analysis on a prepared "hyb" file
                hyb_fold_analysis (pending)         Perform a fold analysis on a prepared "hyb" file
                =================================== =========================================================
                
            These scripts are used on the command line with hyb-format files. For example, to filter a 
            hyb file to contain only hybrids with a sequence identifier containing the string "kshv"::
        
                $ hyb_filter -i my_hyb_file.hyb --filter seg_contains kshv
        
            Further detail on the usage of each script is provided in 
            the |hybkit Toolkit| section of |docs_link|_.
        
        Pipelines:
            Hybkit provides several example pipelines for analysis of "hyb" data using the 
            utilities provided in the toolkit. These include:
            
                ============================= =========================================================
                pipeline                      description
                ============================= =========================================================
                Summary Analysis              Summarize the sequence and miRNA types in a hyb file
                Target Analysis               Analyze targets of a set of miRNA
                Grouped Target Analysis       Analyze targets of a set of miRNA with grouped replicates
                Fold Analysis                 Analyze fold patterns of miRNA-containing hybrids
                Fold Target Region Analysis   Perform fold analysis separated by targeted mRNA region
                ============================= =========================================================
        
            These pipelines provide analysis results in both tabular and graph form.
            As an illustration, the example summary analysis includes the return of 
            the contained hybrid sequence types as both a csv table and as a pie chart:
        
                `CSV Output <https://raw.githubusercontent.com/RenneLab/hybkit/master/sample_01_summary_analysis/example_output/combined_analysis_types_hybrids.csv>`_
        
                |sample_01_image|
        
            Further detail on each provided pipeline can be found in 
            the |Example Pipelines| section of |docs_link|_.
        
        Hybkit API:
            Hybkit provides a Python3 module with a documented API for interacting with 
            records in ".hyb" files. 
            This capability was inspired by the object interactions in the 
            `BioPython Project <https://biopython.org/>`_. The primary utility is provided by 
            objects used to represent hyb records within hyb files. These records are assigned 
            accessible attributes, and can be analyzed using builtin functions. 
            For example, a workflow to print the identifiers of only sequences within a ".hyb" file
            that contain a miRNA can be performed as such::
        
                import hybkit
                in_file = '/path/to/my_hyb_file.hyb'
        
                # Open a hyb file as a HybFile Object:
                with hybkit.HybFile.open(in_file, 'r') as hyb_file:
        
                    # Return each line in a hyb file as a HybRecord object
                    for hyb_record in hyb_file:
        
                        # Analyze each record to assign segment types
                        hyb_record.find_types()
        
                        # If the record contains an miRNA type, print the record identifier.
                        if hyb_record.has_property('segtype_contains', 'miRNA')
                            print(hyb_record.id)
        
            Further documentation on the hybkit API can be found in the 
            |hybkit API| section of |docs_link|_.
        
        Hybkit is still in beta testing. Feedback and comments are welcome to ds@ufl.edu !
        
        
        Installation
        ============
        
        Hybkit requires Python 3.6+ and the use of the 
        `matplotlib <https://matplotlib.org/>`_ package.
        
        The recommended installation method is via hybkit's 
        `PyPI Package Index <https://pypi.org/project/hybkit/>`_ using 
        `python3 pip <https://pip.pypa.io/en/stable/>`_, which will 
        automatically handle version control and dependency installation::
            
            $ pip install hybkit
        
        Acquisition of the package can also be performed by cloning the project's Github repository::
        
            $ git clone git://github.com/RenneLab/hybkit
        
        Or by downloading the zipped package::
        
            $ curl -OL https://github.com/dstrib/hybkit/archive/master.zip
            $ unzip master.zip
        
        Followed by installation using python's setuptools::
        
            $ python setup.py install
        
        Further documentation on hybkit usage can be found in |docs_link|_.
        
        .. |hybkit Toolkit| replace:: *hybkit Toolkit*
        .. |Example Pipelines| replace:: *Example Pipelines*
        .. |hybkit API| replace:: *hybkit API*
        .. |docs_link| replace:: hybkit's ReadTheDocs
        .. _docs_link: https://hybkit.readthedocs.io#
        .. |sample_01_image| image:: sample_01_summary_analysis/example_output/combined_analysis_types_hybrids.png
        
        
Keywords: genetics genomics ribonomics bioinformatics CLASH qCLASH miRNA
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Natural Language :: English
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
