Jellyfish | A fast multi-threaded k-mer counter | Genomics library

 by   gmarcais C++ Version: v2.3.0 License: Non-SPDX

kandi X-RAY | Jellyfish Summary

kandi X-RAY | Jellyfish Summary

Jellyfish is a C++ library typically used in Artificial Intelligence, Genomics applications. Jellyfish has no bugs, it has no vulnerabilities and it has low support. However Jellyfish has a Non-SPDX License. You can download it from GitHub.

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the documentation for details.
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            kandi-support Support

              Jellyfish has a low active ecosystem.
              It has 388 star(s) with 138 fork(s). There are 31 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 89 open issues and 84 have been closed. On average issues are closed in 61 days. There are 8 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of Jellyfish is v2.3.0

            kandi-Quality Quality

              Jellyfish has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              Jellyfish has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              Jellyfish releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.
              It has 1507 lines of code, 44 functions and 15 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

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            Jellyfish Key Features

            No Key Features are available at this moment for Jellyfish.

            Jellyfish Examples and Code Snippets

            No Code Snippets are available at this moment for Jellyfish.

            Community Discussions

            QUESTION

            Bash Shell Script :: Send STD-OUT in Real Time?
            Asked 2022-Mar-06 at 19:38

            At my job, my team and I (we are five people) use a Java program for everyday work. Rather than require everyone to install Java and run the programs on their laptops, I set up a little VM, put the Java code on that, then built a primitive little webpage as an interface. When a colleague pushes a "RUN CODE" button on the webpage, the webpage runs a simple bash shell script:

            ...

            ANSWER

            Answered 2022-Mar-06 at 19:38

            QUESTION

            Connecting frontend with backend
            Asked 2022-Feb-27 at 01:40

            I am creating a react native app that needs to perform registering and authentication of users. I am able to make a POST request that talks to a mongoose server and saves the information in MongoDB. What I want to do now is that when a user inputs their username, email, and password into a textbox screen in React, I want this informaiton to be savedin my MongoDB database. I am having trouble connecting the frontend (React Native) with the backend (MongoDB database).

            Here is the code for my register screen of my React Native App:

            ...

            ANSWER

            Answered 2022-Feb-27 at 01:40

            Your front end needs to be making a call to the endpoint, not locally import the code from your backend.

            What you're doing with postman is correct. Here is what you need to do in your front end:

            Source https://stackoverflow.com/questions/71281393

            QUESTION

            Jupyter notebook truncates value inside of individual cells (not rows or columns, but the text)
            Asked 2022-Feb-19 at 19:20

            Python 3.9.10
            notebook==6.4.8
            Linux VERSION="22.04 (Jammy Jellyfish)"

            I have data including very long UUID strings. Regardless of how many rows or columns are being shown in the Jupyter output, the long UUID strings are being truncated in each individual cell...

            I.e.

            ...

            ANSWER

            Answered 2022-Feb-19 at 19:20

            To see all the full text, you could use pd.set_option('display.max_colwidth', None)

            or if you want to have this for only one display:

            Source https://stackoverflow.com/questions/71034052

            QUESTION

            Discord Selfbot unable to call on_message()
            Asked 2022-Feb-19 at 16:52

            I made a Selfbot on Discord (please do not tell me its against the ToS, I have already been told hundreds of times) to send the string "Hello!" everytime someone sends "!hello", and it can also grind other bots such as Dank Memer, all via an on_message() function. But for some reason, when I run the bot, it can login into the account, but the on_message() doesn't seem to work. There is a print() function called in it which is also not displayed, which means that the bot cannot react to the on_message function. It is currently hosted and run on https://replit.com. Please help, I cannot continue developing it after this.

            Full Code here:

            ...

            ANSWER

            Answered 2022-Feb-19 at 16:52

            Recent Discord API Changes disallows Self-Bots (which is against Discord's ToS) to receive message contents from other users (except itself), hence why your message commands will not work.

            Source https://stackoverflow.com/questions/71181853

            QUESTION

            Compare names on exact overlap at indexed positions
            Asked 2022-Jan-26 at 09:30

            I have a list of names and those that are like "John Smith" vs "J Smith" want to pickup.

            difflib and .intersection here don’t help, Levenstein too. If it is:

            ...

            ANSWER

            Answered 2022-Jan-26 at 09:30

            You can give the following Pythonic implementation a try. No need for fancy levenshtein distance, luckily. In short, split by different words, and then for each potentially matching section check whether:

            • The first characters between the two name sections overlap. If not, then there is no match. (e.g. John and Lucas, J and Lucas or J and L)
            • The two name sections are both longer than 1 character, and are different. If so, then there is no match. (e.g. Jane and John)

            In the cases where these "no match" requirements don't trigger, then there should be an overlap possible. E.g. J and Jane, or Lucas and Lucas. I've included extensive comments on how everything works in code, too.

            Source https://stackoverflow.com/questions/70815565

            QUESTION

            Pip install failing due to pyopenssl / OpenSSL error
            Asked 2022-Jan-07 at 17:24

            I'm running Python 3.8.10 on WSL2 (Windows Subsystem for Linux) in a corporate environment and am encountering the below error, which I believe is related to pyopenssl / OpenSSL, when attempting to install anything using pip. It's not clear to me if I made any system-level changes that led to this strange behavior.

            ...

            ANSWER

            Answered 2022-Jan-07 at 17:24

            From the comments, we ultimately determined that the pip downloads were being blocked by company policy.

            Troubleshooting steps that helped us arrive at the right solution:

            • A ping files.pythonhosted.org was successful, so we next tried ...

            • A manual download of the URI reported by the pip error from the original/updated question:

            Source https://stackoverflow.com/questions/70544278

            QUESTION

            How to fix warning "The 'u' format is deprecated" when using jellyfish package
            Asked 2021-Nov-25 at 10:34

            I am writing a Python script to do name matching. For that I want to use the jellyfish module. But when I run this code:

            ...

            ANSWER

            Answered 2021-Nov-25 at 10:32

            It's just a warning. You can use the package just fine.

            If you don't care to see the warning, you can set up a Python warning filter.

            This has been addressed in https://github.com/jamesturk/jellyfish/issues/131 / https://github.com/jamesturk/cjellyfish/pull/12 and will likely be released in the next version of Jellyfish.

            Source https://stackoverflow.com/questions/70109463

            QUESTION

            How do I make my player image bigger on collision while keeping its proportions?
            Asked 2021-Nov-13 at 22:29

            I am making a game in pygame where you now swim around and eat small squares, with an animation to the jellyfish. I've made it so you get bigger when eating, but when adding a number between 1-9 to the scale the image sort of gets wider than I want it to become. When I have the scale go up by 10 or more when eating this problem does not occur as badly.

            This is the code for the jellyfish/player:

            ...

            ANSWER

            Answered 2021-Nov-13 at 16:16

            Pygame behaves weird when using the transformed image repetitively as in case of rotation...

            I even have faced crashes due to it

            So try using the the same image which is initially loaded as img0,img1,etc. and scale it to the desired size. As of now you were using the same scaled image again and again . This might help

            Source https://stackoverflow.com/questions/69931009

            QUESTION

            Embedding CLIPS into C++ application - interacting with CLIPS from C++
            Asked 2021-Oct-14 at 20:09

            I have compiled CLIPS 6.4 into a shared library (compiled as C++) so that I can use in a C++ application.

            I want to now write a simple test C++ application that allows me to:

            1. Start up the CLIPS engine
            2. Load a CLIPS program (see animal.clp)
            3. Assert a fact from the C++ program to the CLIPS engine and receive responses back from CLIPS in my C++ program
            4. Safely terminate the CLIPS engine and cleanup when nothing on the agenda (all rules fired) - i.e. program completed
            Testapp.cc ...

            ANSWER

            Answered 2021-Oct-14 at 20:09

            The CLIPS Advanced Programming Guide is here: http://clipsrules.sourceforge.net/documentation/v640/apg.pdf

            You can use the Load function (section 3.2.2) to load a file. There is an example of its use in section 3.6.1.

            You can use the GetNextActivation function (section 12.7.1) to determine if the agenda has any activations.

            The simplest way to create facts is using the AssertString function (section 3.3.1). Sections 3.6.2, 4.5.4, and 5.3 have an example use of this function. You can also use the FactBuilder functions described in section 7.1 (with an example in section 7.6.1).

            If the results of your program running are represented by facts, you can use the fact query functions via the Eval function to retrieve those values from your program. Section 4.5.4 has an example.

            Source https://stackoverflow.com/questions/69556981

            QUESTION

            How to compare similarity between two strings (other than English language) in Python
            Asked 2021-Sep-29 at 13:27

            I want to find the similarity between the two strings Example

            ...

            ANSWER

            Answered 2021-Sep-29 at 13:27

            You can use a SequenceMatcher from the built-in module difflib

            Code example:

            Source https://stackoverflow.com/questions/69377194

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

            Vulnerabilities

            No vulnerabilities reported

            Install Jellyfish

            On Debian and Ubuntu with apt:. On Arch, it is available from AUR.

            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 .
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