abyss | : microscope : Assemble large genomes using short reads | Genomics library

 by   bcgsc C++ Version: 2.3.7 License: Non-SPDX

kandi X-RAY | abyss Summary

kandi X-RAY | abyss Summary

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

ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes. Please [cite our papers] #citation).
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              abyss has a low active ecosystem.
              It has 268 star(s) with 100 fork(s). There are 28 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 6 open issues and 312 have been closed. On average issues are closed in 129 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of abyss is 2.3.7

            kandi-Quality Quality

              abyss has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              abyss 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

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

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            abyss Key Features

            No Key Features are available at this moment for abyss.

            abyss Examples and Code Snippets

            No Code Snippets are available at this moment for abyss.

            Community Discussions

            QUESTION

            Invalid argument(s) (input): Must not be null - Flutter
            Asked 2021-May-30 at 11:07

            Am building a movies App where i have list of posters loaded using TMDB using infinite_scroll_pagination 3.0.1+1 library. First set of data loads good but after scrolling and before loading second set of data i get the following Exception.

            ...

            ANSWER

            Answered 2021-May-30 at 10:18

            In Result object with ID 385687 you have a property backdrop_path being null. Adjust your Result object and make the property nullable:

            String? backdropPath;

            Source https://stackoverflow.com/questions/67755803

            QUESTION

            AddForce to local transform
            Asked 2021-May-17 at 01:02

            I'm currently trying to make a game to put my relatively new coding knowledge to test. I figured I learn a lot quicker by just doing things and seeing what happens. I'm currently working on a plane and the last couple of days I made a functional camera system (to rotate around the player based on the mouse) and some animations of the plane. I'm currently trying to create a movement system in which the down key rotates the player up. I noticed however that my AddForce function doesn't do what I want it to do. I'd like the plane to move in the Z axis depending on the current rotation of said plane instead of it just heading into the Z angle of the world.

            I'm currently working on this snippet:

            ...

            ANSWER

            Answered 2021-May-17 at 01:02

            I think the reason your plane is acting strange is not because of your addrelative force call -- it's because you are setting velocity. playerRb.velocity = new Vector3(playerRb.velocity.x, playerRb.velocity.y, -350); assigns the velocity to push you -350 in the world's z axis, which probably isn't what you want. Velocity is in the global space. Remove that and see what happens.

            On a more general note, If you're using physics, try to use only forces and torquees. Using transform.Rotate to change a rigidbody's rotation while physics is active will just make your life difficult, and make the rigidbody do strange things. I do change the velocity of rigidbodies sometimes, but not in every frame. I just don't know enough about physics to mess with velocities that way.

            Also, make sure you're doing these things in a FixedUpdate function, since that is where input that affects physics is supposed to be checked.

            Source https://stackoverflow.com/questions/67562652

            QUESTION

            how to sort structures with string values
            Asked 2021-May-08 at 20:58

            I am trying to sort a dictionary in alphabetical order, which consists of structures with words followed by the meaning. When I run the program, the output for the third structure reads: <

            ...

            ANSWER

            Answered 2021-May-08 at 20:58

            first to compare easily your strings you can use the function strcmp that is in string.h that you already include (take a look at man strcmp for more precision);

            Secondary to sort your "dictionary" you can use the bubble sort algorithm which is a simple and adapted algorithm for your task : bubble sort algorithm, there is explanation and examples that can help you

            Source https://stackoverflow.com/questions/67451681

            QUESTION

            (python, beautifulsoup) When a 'td' contains certain string, take the whole tr
            Asked 2021-Mar-17 at 20:23

            I have a html code that has multiple 'tr' which at the same time every 'tr' has multiple 'td' inside. Im interested in getting only the entire 'tr' that contains a 'td' with a x string and i want the code to filter out all the 'tr' that doesn't contain a 'td' inside with that x string. Is that possible?. I'm new to this and i spent hours looking for a solution but i couldn't.

            Here for example i want to get the entire 'tr' of those that contains a 'td' with string "acid blob"

            ...

            ANSWER

            Answered 2021-Mar-17 at 20:23

            You can locate the td tags and use .find_parent('tr') to move backup to the tr tag.

            (.parent also works here)

            Source https://stackoverflow.com/questions/66679743

            QUESTION

            Python 3: How Do I Invert A Dictionary That Has A List As A Value
            Asked 2021-Mar-15 at 12:16

            So for class I need to take a dictionary that has a list as a value and invert it. I have found several ways to do this, but the issue is when there are non-unique values. I found a way to do this but I feel like there must be much easier and streamlined ways to do this.

            ...

            ANSWER

            Answered 2021-Mar-15 at 12:05

            You can replace your if else :

            Source https://stackoverflow.com/questions/66637332

            QUESTION

            Beautiful soup not returning expected result
            Asked 2021-Jan-31 at 09:04

            I was using beautifulsoup to try to collect information from a website "https://www.yugiohcardguide.com/archetype/abyss-actor.html". The card information is set up relatively neatly. Below is a picture of the html that I was trying to parse through.

            I am trying to get all of the tags that contain the information for a single card in each row.

            below is the code that I used

            ...

            ANSWER

            Answered 2021-Jan-31 at 08:59

            May be this code will helps you:

            Source https://stackoverflow.com/questions/65975939

            QUESTION

            Recommendation System by using Euclidean Distance (TypeError: unsupported operand type(s) for -: 'str' and 'str')
            Asked 2021-Jan-03 at 19:48

            I have a problem about implementing recommendation system by using Euclidean Distance.

            What I want to do is to list some close games with respect to search criteria by game title and genre.

            Here is my project link : Link

            After calling function, it throws an error shown below. How can I fix it?

            Here is the error

            ...

            ANSWER

            Answered 2021-Jan-03 at 16:00

            The issue is that you are using euclidean distance for comparing strings. Consider using Levenshtein distance, or something similar, which is designed for strings. NLTK has a function called edit distance that can do this or you can implement it on your own.

            Source https://stackoverflow.com/questions/65551325

            QUESTION

            Error message when attempting to define a function
            Asked 2020-Dec-18 at 14:27

            Using python on repl.it

            Attempting to define a function, and getting a vague syntax error when trying to run the program. I have attempted to fix this by redoing the indentations, with no luck. Please help. code below

            ...

            ANSWER

            Answered 2020-Dec-18 at 14:27

            I haven't closed the brackets on line 31

            battleaction = str(input('[a]ttack [s]uper attack [i]tem or [r]un')

            Source https://stackoverflow.com/questions/65249534

            QUESTION

            How to display first element of JSON in SwiftUI?
            Asked 2020-Nov-29 at 05:32

            I am new to Swift and IOS development, and I am trying to display fetched JSON data onto a text label.

            Essentially, my goal is to display only the first object of the following API call result onto a text label (see example further down)

            JSON to decode:

            ...

            ANSWER

            Answered 2020-Nov-29 at 05:32

            I assume you wanted this

            Source https://stackoverflow.com/questions/65057188

            QUESTION

            Mesh based collision geometry in drake
            Asked 2020-Oct-04 at 19:38

            I wanted to generate datasets for perception and grasping based on the physics engine. I tried importing following 3D models released by google research recently ( https://app.ignitionrobotics.org/GoogleResearch ) into drake and creating the segmentation dataset for a variety of shoes i.e drop meshes into the bin / let it come to rest and read the rgb / depth and segmentation images.

            However, specifying the object meshes (.obj files) as collision geometry in drake doesn't seem to work since the shoes just penetrate through the bin and keep falling into the abyss (attached snapshot).

            I also noticed that YCB objects have collision geometry described using simple boxes and point contacts. Here is the visualization of the same (as you may be already familiar). Green is the collision geometry.

            If I have to simulate the above do I need to describe simple geometry for all objects from google research dataset ? If so, how were they generated ? Are there some tools one uses to generate this or it was done manually ? or should I enable the hydroelastic contact simulation for this to work when meshes are used for collision geometry ?

            If it can handle any convex mesh, an alternative is to make a convex hull of the original mesh as collision geometry.

            Also as an alternative I tried the same with pybullet. Instead of the bin, I used a plane. Pybullet seems to be handling specifying the mesh as collision geometry correctly through. Here is the snapshot of the data in pybullet.

            An intermediate solution (doesn't address the grasping part yet):

            After discussion with Sean & Russ, I created convex hull of the triangle mesh (using open3D) and it appears that using this convex hull as the collision mesh and annotation to mesh tag, the shoes come to stable pose. I think this solution is good enough for me for generating the perception data using drake. Here is the snapshot after using the solution below:

            ...

            ANSWER

            Answered 2020-Oct-04 at 16:23

            Your observations are spot on.

            Drake doesn't currently support arbitrary meshes for contact (aka the "proximity" role) (only for "illustration" and "perception"). In fact, if the console is available to you, there will probably be warning printed indicating as much. Until that feature is added you have the following options:

            • As you observed in the YCB data, introduce simple primitives to approximate the meshes. Currently, there are no published techniques for generating the simple representations. It's mostly an ad hoc, by-hand approach.
            • Load an OBJ that represents a truly convex polytope and add the tag as the child of the geometry. This will inform Drake to expect a convex mesh which is supported in contact. So, if you can create the convex hull easily, that might be a good direction to go.

            It's difficult to recommend using hydroelastic contact. It's not quite ready for real use and has some restrictions (restrictions which may prove too problematic for you). If you're interested in investigating that further, we can explore that. But for now, I'd recommend some convex representation of your objects.

            Source https://stackoverflow.com/questions/64196799

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

            Vulnerabilities

            No vulnerabilities reported

            Install abyss

            Install [Homebrew](https://brew.sh), and run the command.
            Install [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/) and [Homebrew](https://brew.sh), and run the command.

            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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            https://github.com/bcgsc/abyss.git

          • CLI

            gh repo clone bcgsc/abyss

          • sshUrl

            git@github.com:bcgsc/abyss.git

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