******
hybkit
******
.. image:: https://img.shields.io/github/v/release/RenneLab/hybkit?include_prereleases&logo=github
:target: https://github.com/RenneLab/hybkit/releases
:alt: GitHub release (latest by date including pre-releases)
.. image:: https://img.shields.io/pypi/v/hybkit?logo=pypi&logoColor=white
:target: https://pypi.org/project/hybkit/
:alt: PyPI Package Version
.. image:: https://img.shields.io/conda/vn/bioconda/hybkit?logo=anaconda
:target: http://bioconda.github.io/recipes/hybkit/README.html
:alt: Bioconda Release
.. image:: https://img.shields.io/conda/dn/bioconda/hybkit?logo=Anaconda
:target: http://bioconda.github.io/recipes/hybkit/README.html
:alt: Hybkit Downloads on Bioconda
.. image:: https://img.shields.io/conda/vn/bioconda/hybkit?color=lightgrey&label=Image%20%28quay.io%29&logo=docker
:target: https://quay.io/repository/biocontainers/hybkit?tab=tags
:alt: Docker Image Version
.. image:: https://img.shields.io/circleci/build/github/RenneLab/hybkit?label=CircleCI&logo=circleci
:target: https://app.circleci.com/pipelines/github/RenneLab/hybkit
:alt: Circle-CI Build Status
.. image:: https://img.shields.io/readthedocs/hybkit?logo=read-the-docs
:target: https://hybkit.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://img.shields.io/coveralls/github/RenneLab/hybkit?logo=coveralls
:target: https://coveralls.io/github/RenneLab/hybkit
:alt: Coveralls Coverage
.. image:: https://img.shields.io/pypi/pyversions/hybkit?logo=python&logoColor=white
:target: https://pypi.org/project/hybkit/
:alt: PyPI - Python Version
.. image:: https://img.shields.io/badge/License-GPLv3+-blue?logo=GNU
:target: https://www.gnu.org/licenses/gpl-3.0.en.html
:alt: GNU GPLv3+ License
| Welcome to *hybkit*, a toolkit for analysis of hyb-format chimeric
(hybrid) RNA sequence data defined with the Hyb software package by |Travis2014|_.
This genomic data-type is generated from RNA proximity-ligation and ribonomics
techniques such as Crosslinking, Ligation, and
Sequencing of Hybrids (CLASH; |Helwak2013|_) and quick CLASH (qCLASH; |Gay2018|_).
| This software is available via Github, at http://www.github.com/RenneLab/hybkit .
| Full project documentation is available at |docs_link|_.
Project components:
#. hybkit toolkit of command-line utilities for manipulating,
analyzing, and plotting hyb-format data.
#. The hybkit python API, an extendable documented codebase
for creation of custom analyses of hyb-format data.
#. Integrated analysis of predicted secondary structure (fold) information for
the API and command-line utilities.
#. Example analyses for publicly available qCLASH hybrid
sequence data implemented in each of the command-line scripts and hybkit Python API.
Hybkit Toolkit:
The hybkit toolkit includes several command-line utilities
for manipulation of hyb-format data:
=================================== ===========================================================
Utility Description
=================================== ===========================================================
hyb_check Parse hyb (and fold) files and check for errors
hyb_eval Evaluate hyb (and fold) records to identify / assign
segment types and miRNAs using custom criteria
hyb_filter Filter hyb (and fold) records to a specific
custom subset
hyb_analyze Perform an energy, type, miRNA, target, or fold analysis
on hyb (and fold) files and plot results
=================================== ===========================================================
These scripts are used on the command line with hyb (and associated "vienna" or "CT") files.
For example, to filter a
hyb and corresponding vienna file to contain only hybrids with
a sequence identifier containing the string "kshv":
Example:
::
$ hyb_filter -i my_hyb_file.hyb -f my_hyb_file.vienna --filter any_seg_contains kshv
Further detail on the usage of each script is provided in
the |hybkit Toolkit| section of |docs_link|_.
Hybkit API:
Hybkit provides a Python3 module with a documented API for interacting with
records in hyb files and associated vienna or CT files.
This capability was inspired by the `BioPython Project <https://biopython.org/>`_.
The primary utility is provided by a class for hyb records (HybRecord), a class
for fold records (FoldRecord), and file-iterator classes
(HybFile, ViennaFile, CTFile, HybFoldIter).
Record attributes can be analyzed, set, and evaluated using included class methods.
For example, a workflow to print the identifiers of only sequences within a ".hyb" file
that contain a miRNA can be performed as such::
#!/usr/bin/env python3
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.eval_types()
# If the record contains a long noncoding RNA type, print the record identifier.
if hyb_record.has_prop('any_seg_type_contains', 'lncRNA')
print(hyb_record.id)
Further documentation on the hybkit API can be found in the
|hybkit API| section of |docs_link|_.
Example Analyses:
Hybkit provides several example analyses for hyb data using the
utilities provided in the toolkit. These include:
============================= ===========================================================
Analysis Description
============================= ===========================================================
Type/miRNA Analysis Quantify sequence types and miRNA types in a hyb file
Target Analysis Analyze targets of a set of miRNAs from a single
experimental replicate
Grouped Target Analysis Analyze and plot targets of a set of miRNAs from
pooled experimental replicates
Fold Analysis Analyze and plot predicted miRNA folding patterns in
miRNA-containing hybrids
============================= ===========================================================
These analyses 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/example_01_type_mirna_analysis/example_output/combined_analysis_type_hybrid_types.csv>`_
|example_01_image|
Further detail on each provided analysis can be found in
the |Example Analyses| section of |docs_link|_.
Installation:
Dependencies:
* Python3.8+
* `matplotlib <https://matplotlib.org/>`_ >= 3.7.1 (|Hunter2007|_)
* `BioPython <https://biopython.org/>`_ >= 1.79 (|Cock2009|_)
Via PyPI / Python PIP:
|PipVersion|
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:
.. code-block:: bash
$ python3 -m pip install hybkit
Via Conda:
|CondaVersion| |InstallBioconda|
For users of conda, the hybkit package and dependencies are hosted on the
the `Bioconda <https://bioconda.github.io/>`_ channel, and can be installed
using conda:
.. code-block:: bash
$ conda install -c bioconda hybkit
Via Docker/Singularity:
|DockerVersion|
The hybkit package is also available as a `Docker <https://www.docker.com/>`_
image and `Singularity <https://sylabs.io/singularity/>`_ container, hosted
via the `BioContainers <https://biocontainers.pro/>`_ project on
`quay.io <https://quay.io/repository/biocontainers/hybkit?tab=tags>`_.
To pull the image via docker:
.. code-block:: bash
$ docker pull quay.io/biocontainers/hybkit:0.3.0--pyhdfd78af_0
To pull the image via singularity:
.. code-block:: bash
$ singularity pull docker://quay.io/biocontainers/hybkit:0.3.0--pyhdfd78af_0
Manually Download and Install:
|GithubVersion|
Use git to clone the project's Github repository:
.. code-block:: bash
$ git clone git://github.com/RenneLab/hybkit
*OR* download the zipped package:
.. code-block:: bash
$ curl -OL https://github.com/RenneLab/hybkit/archive/master.zip
$ unzip master.zip
Then install using python setuptools:
.. code-block:: bash
$ python setup.py install
Further documentation on hybkit usage can be found in |docs_link|_.
Copyright:
| hybkit is a free, sharable, open-source project.
| All source code and executable scripts contained within this package are considered
part of the "hybkit" project and are distributed without any warranty or implied warranty
under the GNU General Public License v3.0 or any later version, described in the "LICENSE"
file.
.. |Helwak2013| replace:: *Helwak et al. (Cell 2013)*
.. _Helwak2013: https://doi.org/10.1016/j.cell.2013.03.043
.. |Travis2014| replace:: *Travis et al. (Methods 2014)*
.. _Travis2014: https://doi.org/10.1016/j.ymeth.2013.10.015
.. |Gay2018| replace:: *Gay et al. (J. Virol. 2018)*
.. _Gay2018: https://doi.org/10.1128/JVI.02138-17
.. |Hunter2007| replace:: *Hunter JD. (Computing in Science & Engineering 2007)*
.. _Hunter2007: https://doi.org/10.1109/MCSE.2007.55
.. |Cock2009| replace:: *Cock et al. (Bioinformatics 2009)*
.. _Cock2009: https://doi.org/10.1093/bioinformatics/btp163
.. |PipVersion| image:: https://img.shields.io/pypi/v/hybkit?logo=pypi&logoColor=white
:target: https://pypi.org/project/hybkit/
:alt: PyPI Package Version
.. |InstallBioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&logo=anaconda
:target: http://bioconda.github.io/recipes/hybkit/README.html
:alt: Install with Bioconda
.. |CondaVersion| image:: https://img.shields.io/conda/vn/bioconda/hybkit?logo=anaconda
:target: http://bioconda.github.io/recipes/hybkit/README.html
:alt: Bioconda Release
.. |DockerVersion| image:: https://img.shields.io/conda/vn/bioconda/hybkit?color=lightgrey&label=Image%20%28quay.io%29&logo=docker
:target: https://quay.io/repository/biocontainers/hybkit?tab=tags
:alt: Docker Image Version
.. |GithubVersion| image:: https://img.shields.io/github/v/release/RenneLab/hybkit?include_prereleases&logo=github
:target: https://github.com/RenneLab/hybkit/releases
:alt: GitHub release (latest by date including pre-releases)
.. Github Only
.. |hybkit Toolkit| replace:: *hybkit Toolkit*
.. |Example Analyses| replace:: *Example Analyses*
.. |hybkit API| replace:: *hybkit API*
.. |docs_link| replace:: hybkit's ReadTheDocs
.. _docs_link: https://hybkit.readthedocs.io#
.. |example_01_image| image:: example_01_type_mirna_analysis/example_output/combined_analysis_types_mirna_hybrids.png
Raw data
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"keywords": "genetics,genomics,microRNAs,Ribonomics,Hyb,Hybrids,CLASH,qCLASH,CLEAR-CLIP,Chimeric e-CLIP",
"author": "Daniel Stribling",
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"description": "******\nhybkit\n******\n.. image:: https://img.shields.io/github/v/release/RenneLab/hybkit?include_prereleases&logo=github\n :target: https://github.com/RenneLab/hybkit/releases\n :alt: GitHub release (latest by date including pre-releases)\n.. image:: https://img.shields.io/pypi/v/hybkit?logo=pypi&logoColor=white\n :target: https://pypi.org/project/hybkit/\n :alt: PyPI Package Version\n.. image:: https://img.shields.io/conda/vn/bioconda/hybkit?logo=anaconda\n :target: http://bioconda.github.io/recipes/hybkit/README.html\n :alt: Bioconda Release\n.. image:: https://img.shields.io/conda/dn/bioconda/hybkit?logo=Anaconda\n :target: http://bioconda.github.io/recipes/hybkit/README.html\n :alt: Hybkit Downloads on Bioconda\n.. image:: https://img.shields.io/conda/vn/bioconda/hybkit?color=lightgrey&label=Image%20%28quay.io%29&logo=docker\n :target: https://quay.io/repository/biocontainers/hybkit?tab=tags\n :alt: Docker Image Version\n.. image:: https://img.shields.io/circleci/build/github/RenneLab/hybkit?label=CircleCI&logo=circleci\n :target: https://app.circleci.com/pipelines/github/RenneLab/hybkit\n :alt: Circle-CI Build Status\n.. image:: https://img.shields.io/readthedocs/hybkit?logo=read-the-docs\n :target: https://hybkit.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n.. image:: https://img.shields.io/coveralls/github/RenneLab/hybkit?logo=coveralls\n :target: https://coveralls.io/github/RenneLab/hybkit\n :alt: Coveralls Coverage\n.. image:: https://img.shields.io/pypi/pyversions/hybkit?logo=python&logoColor=white\n :target: https://pypi.org/project/hybkit/\n :alt: PyPI - Python Version\n.. image:: https://img.shields.io/badge/License-GPLv3+-blue?logo=GNU\n :target: https://www.gnu.org/licenses/gpl-3.0.en.html\n :alt: GNU GPLv3+ License\n\n| Welcome to *hybkit*, a toolkit for analysis of hyb-format chimeric\n (hybrid) RNA sequence data defined with the Hyb software package by |Travis2014|_.\n This genomic data-type is generated from RNA proximity-ligation and ribonomics\n techniques such as Crosslinking, Ligation, and\n Sequencing of Hybrids (CLASH; |Helwak2013|_) and quick CLASH (qCLASH; |Gay2018|_).\n| This software is available via Github, at http://www.github.com/RenneLab/hybkit .\n| Full project documentation is available at |docs_link|_.\n\nProject components:\n #. hybkit toolkit of command-line utilities for manipulating,\n analyzing, and plotting hyb-format data.\n #. The hybkit python API, an extendable documented codebase\n for creation of custom analyses of hyb-format data.\n #. Integrated analysis of predicted secondary structure (fold) information for\n the API and command-line utilities.\n #. Example analyses for publicly available qCLASH hybrid\n sequence data implemented in each of the command-line scripts and hybkit Python API.\n\nHybkit Toolkit:\n The hybkit toolkit includes several command-line utilities\n for manipulation of hyb-format data:\n\n =================================== ===========================================================\n Utility Description\n =================================== ===========================================================\n hyb_check Parse hyb (and fold) files and check for errors\n hyb_eval Evaluate hyb (and fold) records to identify / assign\n segment types and miRNAs using custom criteria\n hyb_filter Filter hyb (and fold) records to a specific\n custom subset\n hyb_analyze Perform an energy, type, miRNA, target, or fold analysis\n on hyb (and fold) files and plot results\n =================================== ===========================================================\n\n These scripts are used on the command line with hyb (and associated \"vienna\" or \"CT\") files.\n For example, to filter a\n hyb and corresponding vienna file to contain only hybrids with\n a sequence identifier containing the string \"kshv\":\n\n Example:\n\n ::\n\n $ hyb_filter -i my_hyb_file.hyb -f my_hyb_file.vienna --filter any_seg_contains kshv\n\n Further detail on the usage of each script is provided in\n the |hybkit Toolkit| section of |docs_link|_.\n\n\nHybkit API:\n Hybkit provides a Python3 module with a documented API for interacting with\n records in hyb files and associated vienna or CT files.\n This capability was inspired by the `BioPython Project <https://biopython.org/>`_.\n The primary utility is provided by a class for hyb records (HybRecord), a class\n for fold records (FoldRecord), and file-iterator classes\n (HybFile, ViennaFile, CTFile, HybFoldIter).\n Record attributes can be analyzed, set, and evaluated using included class methods.\n\n For example, a workflow to print the identifiers of only sequences within a \".hyb\" file\n that contain a miRNA can be performed as such::\n\n #!/usr/bin/env python3\n import hybkit\n in_file = '/path/to/my_hyb_file.hyb'\n\n # Open a hyb file as a HybFile Object:\n with hybkit.HybFile.open(in_file, 'r') as hyb_file:\n\n # Return each line in a hyb file as a HybRecord object\n for hyb_record in hyb_file:\n\n # Analyze each record to assign segment types\n hyb_record.eval_types()\n\n # If the record contains a long noncoding RNA type, print the record identifier.\n if hyb_record.has_prop('any_seg_type_contains', 'lncRNA')\n print(hyb_record.id)\n\n Further documentation on the hybkit API can be found in the\n |hybkit API| section of |docs_link|_.\n\nExample Analyses:\n Hybkit provides several example analyses for hyb data using the\n utilities provided in the toolkit. These include:\n\n ============================= ===========================================================\n Analysis Description\n ============================= ===========================================================\n Type/miRNA Analysis Quantify sequence types and miRNA types in a hyb file\n Target Analysis Analyze targets of a set of miRNAs from a single\n experimental replicate\n Grouped Target Analysis Analyze and plot targets of a set of miRNAs from\n pooled experimental replicates\n Fold Analysis Analyze and plot predicted miRNA folding patterns in\n miRNA-containing hybrids\n ============================= ===========================================================\n\n These analyses provide analysis results in both tabular and graph form.\n As an illustration, the example summary analysis includes the return of\n the contained hybrid sequence types as both a csv table and as a pie chart:\n\n `CSV Output <https://raw.githubusercontent.com/RenneLab/hybkit/master/example_01_type_mirna_analysis/example_output/combined_analysis_type_hybrid_types.csv>`_\n\n |example_01_image|\n\n Further detail on each provided analysis can be found in\n the |Example Analyses| section of |docs_link|_.\n\nInstallation:\n Dependencies:\n * Python3.8+\n * `matplotlib <https://matplotlib.org/>`_ >= 3.7.1 (|Hunter2007|_)\n * `BioPython <https://biopython.org/>`_ >= 1.79 (|Cock2009|_)\n\n Via PyPI / Python PIP:\n |PipVersion|\n\n The recommended installation method is via hybkit's\n `PyPI Package Index <https://pypi.org/project/hybkit/>`_ using\n `python3 pip <https://pip.pypa.io/en/stable/>`_, which will\n automatically handle version control and dependency installation:\n\n .. code-block:: bash\n\n $ python3 -m pip install hybkit\n\n Via Conda:\n |CondaVersion| |InstallBioconda|\n\n For users of conda, the hybkit package and dependencies are hosted on the\n the `Bioconda <https://bioconda.github.io/>`_ channel, and can be installed\n using conda:\n\n .. code-block:: bash\n\n $ conda install -c bioconda hybkit\n\n Via Docker/Singularity:\n |DockerVersion|\n\n The hybkit package is also available as a `Docker <https://www.docker.com/>`_\n image and `Singularity <https://sylabs.io/singularity/>`_ container, hosted\n via the `BioContainers <https://biocontainers.pro/>`_ project on\n `quay.io <https://quay.io/repository/biocontainers/hybkit?tab=tags>`_.\n To pull the image via docker:\n\n .. code-block:: bash\n\n $ docker pull quay.io/biocontainers/hybkit:0.3.0--pyhdfd78af_0\n\n To pull the image via singularity:\n\n .. code-block:: bash\n\n $ singularity pull docker://quay.io/biocontainers/hybkit:0.3.0--pyhdfd78af_0\n\n Manually Download and Install:\n |GithubVersion|\n\n Use git to clone the project's Github repository:\n\n .. code-block:: bash\n\n $ git clone git://github.com/RenneLab/hybkit\n\n *OR* download the zipped package:\n\n .. code-block:: bash\n\n $ curl -OL https://github.com/RenneLab/hybkit/archive/master.zip\n $ unzip master.zip\n\n Then install using python setuptools:\n\n .. code-block:: bash\n\n $ python setup.py install\n\n Further documentation on hybkit usage can be found in |docs_link|_.\n\n Copyright:\n | hybkit is a free, sharable, open-source project.\n | All source code and executable scripts contained within this package are considered\n part of the \"hybkit\" project and are distributed without any warranty or implied warranty\n under the GNU General Public License v3.0 or any later version, described in the \"LICENSE\"\n file.\n\n.. |Helwak2013| replace:: *Helwak et al. (Cell 2013)*\n.. _Helwak2013: https://doi.org/10.1016/j.cell.2013.03.043\n.. |Travis2014| replace:: *Travis et al. (Methods 2014)*\n.. _Travis2014: https://doi.org/10.1016/j.ymeth.2013.10.015\n.. |Gay2018| replace:: *Gay et al. (J. Virol. 2018)*\n.. _Gay2018: https://doi.org/10.1128/JVI.02138-17\n.. |Hunter2007| replace:: *Hunter JD. (Computing in Science & Engineering 2007)*\n.. _Hunter2007: https://doi.org/10.1109/MCSE.2007.55\n.. |Cock2009| replace:: *Cock et al. (Bioinformatics 2009)*\n.. _Cock2009: https://doi.org/10.1093/bioinformatics/btp163\n.. |PipVersion| image:: https://img.shields.io/pypi/v/hybkit?logo=pypi&logoColor=white\n :target: https://pypi.org/project/hybkit/\n :alt: PyPI Package Version\n.. |InstallBioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&logo=anaconda\n :target: http://bioconda.github.io/recipes/hybkit/README.html\n :alt: Install with Bioconda\n.. |CondaVersion| image:: https://img.shields.io/conda/vn/bioconda/hybkit?logo=anaconda\n :target: http://bioconda.github.io/recipes/hybkit/README.html\n :alt: Bioconda Release\n.. |DockerVersion| image:: https://img.shields.io/conda/vn/bioconda/hybkit?color=lightgrey&label=Image%20%28quay.io%29&logo=docker\n :target: https://quay.io/repository/biocontainers/hybkit?tab=tags\n :alt: Docker Image Version\n.. |GithubVersion| image:: https://img.shields.io/github/v/release/RenneLab/hybkit?include_prereleases&logo=github\n :target: https://github.com/RenneLab/hybkit/releases\n :alt: GitHub release (latest by date including pre-releases)\n\n.. Github Only\n.. |hybkit Toolkit| replace:: *hybkit Toolkit*\n.. |Example Analyses| replace:: *Example Analyses*\n.. |hybkit API| replace:: *hybkit API*\n.. |docs_link| replace:: hybkit's ReadTheDocs\n.. _docs_link: https://hybkit.readthedocs.io#\n.. |example_01_image| image:: example_01_type_mirna_analysis/example_output/combined_analysis_types_mirna_hybrids.png\n",
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