Clinker | Gene Fusion Visualiser

 by   Oshlack Python Version: v1.32 License: MIT

kandi X-RAY | Clinker Summary

kandi X-RAY | Clinker Summary

Clinker is a Python library. Clinker has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However Clinker build file is not available. You can download it from GitHub.

Fusion Super Transcript generator and Plotter. Please refer to the wiki for further information & documentation.
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              Clinker has a low active ecosystem.
              It has 37 star(s) with 11 fork(s). There are 6 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 11 open issues and 11 have been closed. On average issues are closed in 54 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of Clinker is v1.32

            kandi-Quality Quality

              Clinker has 0 bugs and 0 code smells.

            kandi-Security Security

              Clinker has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              Clinker code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              Clinker is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              Clinker releases are available to install and integrate.
              Clinker has no build file. You will be need to create the build yourself to build the component from source.
              Clinker saves you 276 person hours of effort in developing the same functionality from scratch.
              It has 668 lines of code, 24 functions and 5 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed Clinker and discovered the below as its top functions. This is intended to give you an instant insight into Clinker implemented functionality, and help decide if they suit your requirements.
            • Create annotation file
            • Generate a bed line for this feature
            • Annotate the fusion line
            Get all kandi verified functions for this library.

            Clinker Key Features

            No Key Features are available at this moment for Clinker.

            Clinker Examples and Code Snippets

            No Code Snippets are available at this moment for Clinker.

            Community Discussions

            QUESTION

            JEP 412: Pass a on-heap byte array to native code, getting UnsupportedOperationException: Not a native address
            Asked 2021-Nov-12 at 14:23

            All this is with the new JDK 17.

            I'm attempting to turn an on-heap byte array into a MemorySegment and pass that to a native function. I created simple sample code that shows this:

            ...

            ANSWER

            Answered 2021-Nov-12 at 14:23

            I thought that one of the major advantages of Project Panama would be that native code could access on-heap memory, to avoid having to copy.

            Actually despite the major advance in usability coming with project Panama, this won't be possible, for multiple reasons.

            • GC moves things around in the Java heap memory, hence the address of any object (including tables) may/will change over time. However the native code is given a pointer to a memory address which of course won't be updated after a GC cycle (not even mentioning accessing that memory in the middle of a cycle).
            • JNI had APIs to actually prevent GC from happening while in the middle of native code through Get*Critical sections. Unfortunately preventing the GC may have significant impact on application performance.

            In fact Project Panama is exactly trying to avoid blocking the GC. This is why there's a clear separation of the accessed memory and why it is necessary to copy to/from native memory.

            This shouldn't be much of an issue, unless this is hot code path (ie it's called very very often), or the code deals with very big data. In such case the code may want to do most of the work off-heap. If the data is in a file, maybe access that file from native code, or use a panama memory mapped file.

            Source https://stackoverflow.com/questions/69521289

            QUESTION

            Error when calling biosphere flows an activity in ecoinvent v.3.5
            Asked 2020-May-25 at 08:36

            I happen to face an error when I try to call the biosphere flows of activity. And When I call the technosphere for different activities, it works fine.

            However, for the biosphere:

            ...

            ANSWER

            Answered 2020-May-25 at 08:36

            There is something wrong with your biosphere3 database - your clinker object has an exchange with the biosphere flow (activity) ('biosphere3', 'fc1c42ce-a759-49fa-b987-f1ec5e503db1') (which is Water, cooling, unspecified natural origin on my machine). However, you are either missing the biosphere3 database entirely, or have deleted or otherwise modified this specific flow.

            The easiest way to fix this is to reinstall it:

            Source https://stackoverflow.com/questions/61972221

            QUESTION

            There has been an error in the installation of petcs. How to solve it?
            Asked 2020-Apr-16 at 03:38

            Computer configuration: my computer is maosx system, in the virtual machine installed ubuntu, the original system install ladder (VPN), Linux did not install a successful ladder (VPN).

            Environment configuration: install petsc in the virtual machine, download and unpack petsc software package, install GCC, gfortran, and download MPI and BLAS/LAPACK separately before, but there was an error when installing MPI. .

            ...

            ANSWER

            Answered 2020-Apr-15 at 18:33

            As Satish said in email, your machine likely ran out of memory. gfortran can take more the 2GB of RAM when compiling. An alternative, if you do not need Fortran, is to configure using --with-fc=0.

            Source https://stackoverflow.com/questions/61232815

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install Clinker

            You can download it from GitHub.
            You can use Clinker like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries
            CLONE
          • HTTPS

            https://github.com/Oshlack/Clinker.git

          • CLI

            gh repo clone Oshlack/Clinker

          • sshUrl

            git@github.com:Oshlack/Clinker.git

          • Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link