nucleus | Python and C++ code for reading and writing genomics data | Genomics library

 by   google C++ Version: 0.6.0 License: Non-SPDX

kandi X-RAY | nucleus Summary

kandi X-RAY | nucleus Summary

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

Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework, as anywhere a genomics file is consumed or produced, a TensorFlow tfrecords file may be used instead.

            kandi-support Support

              nucleus has a low active ecosystem.
              It has 734 star(s) with 124 fork(s). There are 59 watchers for this library.
              It had no major release in the last 12 months.
              There are 0 open issues and 38 have been closed. On average issues are closed in 119 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of nucleus is 0.6.0

            kandi-Quality Quality

              nucleus has no bugs reported.

            kandi-Security Security

              nucleus has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              nucleus 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

              nucleus releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of nucleus
            Get all kandi verified functions for this library.

            nucleus Key Features

            No Key Features are available at this moment for nucleus.

            nucleus Examples and Code Snippets

            No Code Snippets are available at this moment for nucleus.

            Community Discussions


            Coding challenge: Calculate sum of col values if rows in other col are TRUE (table summary)
            Asked 2021-Jan-30 at 00:44

            We have a table where the first col contains values (protein counts) while the following cols are logical vectors (T or F, indicating if protein_id has the property). For each col we seek the sum of all values where col = T and the count of T.

            With example data the task might be better to describe:

            [please excuse that the example data require a package for the random id generator, if you know a base R solution please wrote comment and I will include it here].



            Answered 2021-Jan-30 at 00:44

            Is this what you're looking for? (Code below has been edited!)



            What are the spring provided components?
            Asked 2021-Jan-04 at 20:55

            I m reading a book about spring 5 certifications.

            I have read the following sentence The Spring Framework IoC component is the nucleus of the framework. It uses dependency injection to assemble Spring-provided (also called infrastructure components) and development-provided components to rapidly wrap up an application.

            I believe that development-provided components are my annotated java classes that will be injected using DI for example a @Controller or a @Repository.

            However I m curious about the second part: Infrastructure Components. what are these. where they are being injected ? can I consider the AuthenticationManagerBuilder an Infrastructure Component or are they referencing to another thing?




            Answered 2021-Jan-04 at 20:55

            After the completion of this book chapter

            I conclude that some provided spring components that bootstraps the spring application are like below:

            • org.springframework.context.annotation.internalConfigurationAnnotationProcessor
            • org.springframework.context.annotation.internalAutowiredAnnotationProcessor
            • org.springframework.context.annotation.internalCommonAnnotationProcessor

            and more .



            Best way extract mention from text with link like wikipedia dump
            Asked 2020-Dec-06 at 10:34

            I got data from Wikipedia dump like below:



            Answered 2020-Dec-06 at 10:17

            You should be able to capture those values using re.findall:



            How to get past missing dependencies building Zxing android app?
            Asked 2020-Dec-03 at 12:51

            I am trying to build the Zxing android app (not the libraries) using the instructions here. I was able to build the jars but cannot build the app itself. When I run mvn package android:apk I get the following error:



            Answered 2020-Dec-03 at 11:56

            Check if you haven't missed tag around dependencies.

            Also you can check this answer for better understanding.



            supsample from list of data frames entries with "character"
            Asked 2020-Oct-29 at 19:16

            I got a list that contains 9 data frames and each data frame contains the following lines:



            Answered 2020-Oct-29 at 19:16

            As commented, your earlier search returns an empty data frame since the searched term is part of the larger strings in the character column, GO_NAME. Therefore, instead of == or%in% operators which expects whole word matches, consider grep to search string patterns within larger string:



            How can I add individual data points to my bar plot using ggbarplot? (add jitter does not work, neither does dotplot)
            Asked 2020-Oct-07 at 18:23

            I am having a hard time adding individual data points on my barplots using ggbarplot. I seem to have an issue particularly on multi-grouped data (using fill or color). I've tried a couple different ways to add dots, but they've either resulted in an error (adding jitter) or the dots are not properly aligned to the correct bar (adding dotplot). Any help would be greatly appreciated.

            Example data:



            Answered 2020-Oct-07 at 18:23

            The issue is that with add.params(color = "black") you are overwriting the grouping (color = "Group") needed for dodging the points. Hence, dropping add.params(color = "black") will make your code work. If you want black points and error bars you can do that via e.g. scale_color_manual by setting the colors for all groups to "black":



            Payara server not starting
            Asked 2020-Sep-16 at 11:12

            I'm trying out some Java EE and I can get my code to run on Glassfish 5.0.1 no problem. I want to run it on Payara but I can only get Payara Micro to work, the full and web-profile both crash and give the following errors that I cant find any info about. The closest related problem I could find told me to try changing my path to Java 8 instead, but that had no effect. Thanks!



            Answered 2020-Sep-16 at 11:12

            This happens because your security provider doesn't support the JCEKS algorithm to open the Payara keystore. Try using a different distribution of Java, e.g. AdoptOpenJDK ( It's possible that your Java doesn't support that algorithm.

            The reason why Payara Server fails and GlassFish doesn't is that Payara Server attempts to find configuration values in password aliases, which are protected by the keystore. This results in an exception because it can't open the keystore. I bet that GlassFish would also fail to open the keystore if it needed it at some point later. GlassFish just doesn't have the functionality of reading the configuration from password aliases and thus doesn't attempt to open the keystore at startup.

            Anyway, it's definitely a bug that this exception brings down the whole server. Payara Server should just ignore the configuration and go on. Raise this as a bug in Payara bug tracker:



            Object Mesh Orbiting Opposite Direction of Rendered Image
            Asked 2020-Aug-29 at 00:35

            I am attempting to recreate a Flash website using Three.JS but have run into a snag attempting to create some of the functionality.

            What should be happening is that I want to have some button images orbit around the center of the screen. They should be able to be stopped if the mouse hovers over them and then clicked to open up a different location on the website.

            I have everything working up until the requirement that the buttons stop when the mouse is hovering over them. I am attempting to implement this using a raycast, however when I am moving the mouse around the scene it seems as though the mesh is not at the same place as the rendered texture. In fact it almost seems like the mesh and the rendered image are orbiting in the opposite direction from each other.

            Here is my code and I will link you to a page on my website where I am testing this revamp at so you can get a real-world example:



            Answered 2020-Aug-29 at 00:35

            For starters, your mouseMove() is missing the negative sign before the y-value calculation. This means your y-value gets flipped (it's -1 when it should be +1) It should be as follows:



            Creating figure with multiple box plots in ggplot2
            Asked 2020-Aug-25 at 16:46

            I have some issues trying to plot multiple boxplots in single figure using ggplot, even though I can easily do that in vanilla R. I tried to google for answers for quite a few hours, but I couldn't find anyone who had same problem as me.

            So basically, I have a data frame with 25 columns



            Answered 2020-Aug-25 at 15:17

            If you use ggplot and bring your data into a tidy form (i.e. long format), you can use easily use ggplot to plot several boxplots at once, as suggested in the comments.

            I'm not sure if I completely understand what you're after, but if you want one boxplot per compartiment, combining the gene expression of all genes present in said compartiment, this is a possible solution (I didn't use all your data as it is quite an effort to get it into R in the way you present it):



            SLURM batch script doesn't execute Python script, returns no error message and doesn't stop running
            Asked 2020-Aug-15 at 12:34

            In a SLURM cluster I am submitting a shell script that calls a python script (both scripts can be found below. When the shell script executes it get until where the python script is called but then nothing happens: there is no output, no error message and the SLURM job keeps running.

            I assume the entire contents of the python script are not relevant (but I included it anyway for completion). For debugging purposes I inserted the print("script started") line at the very beginning to see if it gets run but it doesn't. The last thing I see in the output is moved to directory.

            I tried calling a script containing print("test")right before this and it gets executed normally.

            What could be the reason the python script doesn't start and how can I fix it?

            Edit: As user jakub recommended changing print("script started")to print("script started", flush=True)successfully gets printed. Including several more of these statements revealed that the script was actually running perfectly fine, it just didn't output anything. Including the same statement within the for loop that gets constantly executed also makes all print() statements previously missing get printed.

            The question then turns into: why do the print() statements here need to have flush=True in this script but not in other scripts?

            Shell script:



            Answered 2020-Aug-15 at 12:34

            Python buffers stdin, stdout, and stderr by default. print() writes to stdout by default, so you will see this buffered behavior.

            From :

            Python opens the stdin, -out and -error streams in a buffered mode; it'll read or write in larger chunks, keeping data in memory until a threshold is reached.

            You can forcibly flush this buffer by passing flush=True to print. See the documentation for more information. If you have multiple print statements in a row, you need only use flush=True in the last one.


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


            No vulnerabilities reported

            Install nucleus

            Nucleus currently only works on modern Linux systems using Python 3. It must be installed using a version of pip less than 21. To determine the version of pip installed on your system, run. To install Nucleus, run. Note that Nucleus doesn't yet work with Python 3.8. Also, you can ignore any "Failed building wheel for google-nucleus" error messages -- these are expected and won't prevent Nucleus from installing successfully. If you are using Python 2, instead run.


            Overview.Summary of example programs.Python API Reference.
            Find more information at:

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

            Find more libraries

            Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link