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https://github.com/jakobilab/circhemy

Convert and query IDs of circular RNAs from many different databases
https://github.com/jakobilab/circhemy

circrna circular circularrna conversion converter naming-pattern rna

Last synced: 3 months ago
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Convert and query IDs of circular RNAs from many different databases

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README 

          
**circhemy**

======================================================================



**The alchemy of circular RNA ID conversion**



.. image:: https://github.com/jakobilab/circhemy/raw/main/circhemy/web/static/logo_small.png

   :alt: circhemy - The alchemy of circular RNA ID conversion

   :target: https://circhemy.jakobilab.org/



|downloads| |pypi| |ci| |docker|



Introduction

-------------



Circular RNAs (circRNAs) originate through back-splicing events from linear

primary transcripts, are resistant to exonucleases, typically not

polyadenylated, and have been shown to be highly specific for cell type and

developmental stage.



The prediction of circular RNAs is a multi-stage bioinformatics process starting

with raw sequencing data and usually ending with a list of potential circRNA

candidates which, depending on tissue and condition may contain hundreds to

thousands of potential circRNAs. While there are a number of tools for the

prediction process (e.g. circtools developed by our group) a unified naming

convention for circRNA is not available.



Multiple databases gathered hundreds of thousands of circRNAs, however, most

databases employ their own naming scheme, making it harder and harder to keep

track of known circRNAs and their identifiers.



Circhemy

-------------



We developed circhemy, a modular, Python3-based framework for circRNA ID

conversion that unifies several functionalities in a single Python package.

Three different routes are implemented within package to access more than 2

million circRNA IDs:



* User-friendly web application at `circhemy.jakobilab.org `__

* Streamlined CLI application for direct access to the prepackaged local SQLite3 database

* A public `REST API `__ that enables direct access to the most recent ID database from HPC systems using curl or similar tools



Circhemy includes two different modes of action: ``convert`` and ``query``. Convert

allows the user to convert from one type of circRNA ID to a wide variety of

other database identifiers, while query allows users to run direct queries on

the circRNA database to extract circRNAs fulfilling a user-defined set of

constraints.



Moreover, circhemy is the first circRNA resource that supports and integrates

the first version of the **C**\ircRNA **S**\tandard **N**\omenclature (abbreviated

**CSNv1** in circhemy) as outlined in `"A guide to naming eukaryotic circular RNAs", Chen et al. 2023 `__.



Currently, circhemy contains computationally generated CSNv1 names for nearly 1

million circRNAs of Human, mouse, and rat.



Installation

-------------



The circhemy CLI package is written in Python3 (>=3.8) and consists of two

core modules, namely ``convert`` and ``query``. The command line version requires

only one external dependency, ``sqlite3``, for access to the internal SQLite3

database with circRNA ID data



Installation is managed through ``python3 -m pip install circhemy`` or ``python3 setup.py

install`` when installed from the cloned GitHub repository. No sudo access is

required if the installation is executed with ``--user`` which will install the

package in a user-writeable folder. The binaries should be installed

to ``/home/$user/.local/bin/`` in case of Debian-based systems.



circhemy was developed and tested on Debian Buster, but should run with

any other distribution.



The latest release version of circhemy can be installed via pip:



.. code-block:: console



    python3 -m pip install circhemy



Additionally, this repository offers the latest development version:



.. code-block:: console



    python3 -m pip install git+https://github.com/jakobilab/circhemy.git



Command Line Interface

-----------------------



Circhemy currently offers two modules:



Convert module

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The convert module is able to convert from a range of input circRNA ID into different one or more database identifiers.



Example: Convert a list of CircAtlas2 IDs read via STDIN from file input.csv into Circpedia2 IDs, but also output  CircAtlas2 IDs, while writing the output to /tmp/output.csv:



.. code-block:: console



    cat input.csv | circhemy convert -q STDIN -i CircAtlas2 -o Circpedia2 CircAtlas2 -O /tmp/output.csv



Query module

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The query module is able to retrieve circRNA IDs from the internal database that fulfil a set of user-defined constraints.



Example: Retrieve a list of circbase and CircAtlas2 circRNA IDs that are located on chromosome 3 of the species rattus norvegicus; only print out circRNAs from the rn6 genome build.



.. code-block:: console



    circhemy query -o circbase CircAtlas2 -C chr3 -s rattus_norvegicus -g rn6



Representational State Transfer Interface (REST)

-------------------------------------------------



Representational State Transfer, or REST for short, allows users and software

developers to easily access circhemy from within their own tools or pipelines.

Circhemy's REST API uses JSON for input queries and returning output, making it

easy to format queries from every programming language or even by hand.



The REST API it publicly available and uses a fixed set of keywords to perform

conversions or queries. Two examples for the two different modes of action are

shown below.



Convert module

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The convert module is able to convert from a range of input circRNA ID into

different one or more database identifiers.



Example: Convert a list of CircAtlas2 IDs into circBase and

into Circpedia2 IDs, including the Genome build.



.. code-block:: console



    curl -X 'POST' 'https://circhemy.jakobilab.org/api/convert'

      -H 'accept: application/json'

      -H 'Content-Type: application/json'

      -d '{

          "input": "CircAtlas2",

          "output": ["Circpedia2","CircAtlas2","Genome"],

          "query": ["hsa-MYH9_0004","hsa-MYH9_0004"]

          }'



Output is returned as JSON-formatted string which can directly be used for AG

Grid tables for any other postprocessing:



.. code-block:: json



    {

      "columnDefs": [

        {

          "headerName": "circBase",

          "field": "circBase"

        },

        {

          "headerName": "Circpedia2",

          "field": "Circpedia2"

        }

        {

          "headerName": "Genome",

          "field": "Genome"

        }

      ],

      "rowData": [

        {

          "circBase": "hsa_circ_0004470",

          "Circpedia2": "HSA_CIRCpedia_36582"

          "Genome": "hg38"

        },

        {

          "circBase": "hsa_circ_0004470",

          "Circpedia2": "HSA_CIRCpedia_36582"

          "Genome": "hg19"

        }

      ]

    }



Query module

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



The query module is able to retrieve circRNA IDs from the internal database that

fulfil a set of user-defined constraints.



Example: Retrieve all circRNAs with a CircAtlas2 ID containing *nppa* in the

species homo sapiens, return the IDs in circBase and CircAtlas2 format:



.. code-block:: console



                curl -X 'POST'

                  'https://circhemy.jakobilab.org/api/query'

                  -H 'accept: application/json'

                  -H 'Content-Type: application/json'

                  -d '{

                      "input": [

                        {

                          "query": "nppa",

                          "field": "CircAtlas2",

                          "operator1": "AND",

                          "operator2": "LIKE"

                        },

                        {

                          "query": "homo_sapiens",

                          "field": "Species",

                          "operator1": "AND",

                          "operator2": "is"

                        }

                      ],

                      "output": [

                        "circBase",

                        "CircAtlas2"

                      ]

                    }'



Output is returned as JSON-formatted string which can directly be used for AG

Grid tables for any other postprocessing:



.. code-block:: json



    {

      "columnDefs": [

        {

          "headerName": "circBase",

          "field": "circBase"

        },

        {

          "headerName": "CircAtlas2",

          "field": "CircAtlas2"

        }

      ],

      "rowData": [

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA_0001"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA_0002"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA-AS1_0001"

        },

        {

          "circBase": "hsa_circ_0009871",

          "CircAtlas2": "hsa-NPPA-AS1_0004"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA-AS1_0002"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA-AS1_0003"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA_0001"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA_0002"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA-AS1_0001"

        },

        {

          "circBase": "hsa_circ_0009871",

          "CircAtlas2": "hsa-NPPA-AS1_0004"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA-AS1_0002"

        },

        {

          "circBase": "",

          "CircAtlas2": "hsa-NPPA-AS1_0003"

        }

      ]

    }



.. |downloads| image:: https://pepy.tech/badge/circhemy

    :alt: Python Package Index Downloads

    :scale: 100%

    :target: https://pepy.tech/project/circhemy



.. |pypi| image:: https://badge.fury.io/py/circhemy.svg

    :alt: Python package version

    :scale: 100%

    :target: https://badge.fury.io/py/circhemy



.. |ci| image:: https://github.com/jakobilab/circhemy/actions/workflows/run_circhemy_ci.yml/badge.svg

    :alt: CI tests

    :scale: 100%

    :target: https://github.com/jakobilab/circhemy/actions/workflows/run_circhemy_ci.yml



.. |docker| image:: https://github.com/jakobilab/circhemy/actions/workflows/build_docker.yml/badge.svg

    :alt: Docker build process

    :scale: 100%

    :target: https://github.com/jakobilab/circhemy/actions/workflows/build_docker.yml



About

-------------

Circhemy is developed at the `Jakobi Lab `__, part of

the `Translational Cardiovascular Research Center (TCRC) `__, in the Department of Internal Medicine at `The University of Arizona College of Medicine – Phoenix `__.



Contact: **circhemy@jakobilab.org**