Rosalind | Rosalind Bioinformatics Problems | Machine Learning library

 by   cdeterman Python Version: Current License: No License

kandi X-RAY | Rosalind Summary

kandi X-RAY | Rosalind Summary

Rosalind is a Python library typically used in Artificial Intelligence, Machine Learning applications. Rosalind has no bugs, it has no vulnerabilities and it has low support. However Rosalind build file is not available. You can download it from GitHub.

These are my current solutions to the Rosalind Problems. I am very fond of the Biopython toolset and try to apply it where appropriate. As such, implementation of many of these solutions require its' installation. I have tried to annotate my code and notify where installations may be necessary. I generally work with Python 2.7 however I will work towards Python 3.X functionality. I would like to create solutions with other programming languages but primarily these will consist of only python solutions.
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              Rosalind has a low active ecosystem.
              It has 24 star(s) with 17 fork(s). There are 7 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              Rosalind has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of Rosalind is current.

            kandi-Quality Quality

              Rosalind has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              Rosalind does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              Rosalind releases are not available. You will need to build from source code and install.
              Rosalind has no build file. You will be need to create the build yourself to build the component from source.
              Rosalind saves you 593 person hours of effort in developing the same functionality from scratch.
              It has 1382 lines of code, 52 functions and 55 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed Rosalind and discovered the below as its top functions. This is intended to give you an instant insight into Rosalind implemented functionality, and help decide if they suit your requirements.
            • r Reverse substring .
            • Set project defaults .
            • Combine the minimum number of elements in a set of bks .
            • BFS implementation of Rosalind index .
            • Reverse permutation .
            • Return the longest subsequence of a sequence .
            • Reverse permutation .
            • Reverse reverse_perm .
            • Computes the probability for a given domain .
            • Backtrack the given sequence matrix .
            Get all kandi verified functions for this library.

            Rosalind Key Features

            No Key Features are available at this moment for Rosalind.

            Rosalind Examples and Code Snippets

            No Code Snippets are available at this moment for Rosalind.

            Community Discussions

            QUESTION

            Re-initialized state
            Asked 2021-Apr-22 at 09:52

            I have a complex component with some "dynamic" imports.

            I recreate my component tree on codesandbox: https://codesandbox.io/s/clever-rosalind-t3cfm?file=/src/App.js:298-302

            I have an App.js file where I have a list of objects. Each object, render a RenderWidget component.

            Inside RenderWidget, I need to get a "dynamic" comp. (I recreated that with a simple function, but i have more complexity in that part). So I wrapped the comp on useMemo to avoid component re-creation. (useMemo has a console.log to check if the Comp is re-initializated)

            Inside the Comp, we have a useState declaration with the following initial value:

            ...

            ANSWER

            Answered 2021-Apr-22 at 09:51

            If parent component props have changed it will re-render all of its children, you can use React.memo to prevent unnecessary re-render.

            I also suggest you to read this article, it's written by the author of the react core team, in addition to memo, there are other ways to prevent re-rendering

            Source https://stackoverflow.com/questions/67210608

            QUESTION

            Good way to interact between different and same levels of depth (nested) in ReactJS ('States' + Hooks)
            Asked 2021-Apr-21 at 17:43

            I have a ReactJS code (attached at the end of the post) where my objective is to find a good way to be able to "communicate" between some nested elements (I've tried to do a very simple code to explain my idea).

            The columns are "hierarchy" based, so you have to active "A) Parent" before being able to active "A) Child 1". The main objective is to be able to "disable" (basically, set the state 'active' into false) an element when:

            • Some element of a "different column" is active
            • Some element of the same column and "depth" is active

            Some examples based on the code:

            • Disable 'A) Parent' when 'B) Parent' is turned active.
            • Disable 'A) Child 1' when 'A) Child 2' is turned active.
            • Disable 'A) Child 1' (and 'A) Parent') when 'B) Parent' is turned active.

            In this last example, we are also disabling the "ancestors" (since this "works" as a nested structure, where you have to turn on A) Parent to be able to turn on A) Child X ).

            As you can see, the idea is to work on a depth level.. Where when you "enter" in another "path", the current active path should be disabled.

            I've been trying some methods, but none of them have worked properly. I think they are "expensive" and zero elegant.

            My approaches have been something similar to this:

            • Give a "depth var" on each element.
            • Set a "current" var (useState) to App (root) and pass the "setCurrent" to each element.
            • Use a "useEffect" hook inside each looking for changes on current.
            • Then, conditionally try to manage them.

            As I have said.. I'm pretty sure there are better methods to do this.. But I can't get with them.

            Here is the code (for the example, I've tried to do the most simple setup without depth restriction, but remember that you have to "active" the ancestor before being able to "active" the descendant): https://codesandbox.io/s/optimistic-rosalind-1oykv?file=/src/App.js

            ...

            ANSWER

            Answered 2021-Apr-21 at 17:43

            As @Shawn Yap has mentioned in the comments, finally I've opted for using Context Api.

            Basically the idea is the following (very simplified):

            1. Create a React Context:

            Source https://stackoverflow.com/questions/67141220

            QUESTION

            How to pass a property from an array to each of it nested child array with lodash?
            Asked 2021-Apr-20 at 16:18

            Hello let's take this example :

            ...

            ANSWER

            Answered 2021-Apr-20 at 16:18

            When it comes to performance, I always find that vanilla JS is faster than any library implementation. So I always prefer vanilla JS for this reason. Here, a non-lodash.js solution, that places the desired values into the array, though you can simply deep-clone your original array:

            Source https://stackoverflow.com/questions/67182394

            QUESTION

            input event changes after the event handler being debounced
            Asked 2021-Apr-08 at 01:19

            I have a simple form and a field to render the value of that input field from that form

            ...

            ANSWER

            Answered 2021-Apr-08 at 01:19

            The problem comes from the behavior of the input event. The instance of InputEvent comes with the corresponding input element as target, even if you add a listener on the form element.

            So, simply rewrite your code as:

            Source https://stackoverflow.com/questions/66995972

            QUESTION

            Non-exhaustive patterns in function distance error stemming from where statement that shouldn't be reached
            Asked 2021-Mar-01 at 00:46

            I'm learning Haskell and working on a Hamming distance exercise.

            ...

            ANSWER

            Answered 2021-Mar-01 at 00:46

            This error isn't anything to do with your guards - it's much more basic than that.

            You have:

            Source https://stackoverflow.com/questions/66415242

            QUESTION

            Mouseover parallax effect on Vue.js
            Asked 2021-Feb-01 at 09:14

            Good day guys! I want to do mouseover effect like in this video in my vue project. I tried some code but property transform changed just once. If someone knows, please help me. thats codesandbox.io code. I copied just a part of my code which doesn't work.

            ...

            ANSWER

            Answered 2021-Jan-31 at 16:54

            I think better to use the npm library for it with the name vue-kinesis.

            But if you want to use your variant, you need to change line 57:

            Source https://stackoverflow.com/questions/65980986

            QUESTION

            Reactive Vue Router object by wrapping in ref() not working
            Asked 2020-Dec-13 at 11:36

            I have an application where I would like to print the location of the user similar to a breadcrumb. I have a component that I add at the application level and expect it to update with current value or the router.currentRoute object. However it doesn't seem to be updating as expected.

            I'm using the Vue2 Composition api plugin and am trying hard to keep it in a decent state that will make migrating to Vue3 much easier once I'm able. This means I'd like to avoid using the context.$route object that's available. My attempt currently imports the router directly and wraps the currentRoute object in a ref() but that doesn't seem to work.

            Here is a CodeSandbox with an application that shows the issue. I have a home page and two additional pages. The text that reads 'Your current location is: Home` should change to the name of the other pages when navigating there, however it does not change at all.

            ...

            ANSWER

            Answered 2020-Dec-13 at 11:36

            You could use reactive() on the router instance, and then toRef() on that to get currentRoute:

            Source https://stackoverflow.com/questions/65210203

            QUESTION

            How to find all occurrences of a non - contiguous substring in Python?
            Asked 2020-Nov-21 at 12:55

            Premise:

            I am currently working on the following problem:

            http://rosalind.info/problems/sseq/

            I must find the index combinations of all occurrences of a substring in a string, where the substring is not necessarily contiguous.

            My testing parameters:

            ...

            ANSWER

            Answered 2020-Nov-21 at 10:28

            I'm not sure your algorithm could find all solutions even if it would be fixed. I tried this logic instead : Find the initial sequence closest to the left of dna and search all declinations going from right to left recursively. This way the solutions are automatically sorted.

            Source https://stackoverflow.com/questions/64862256

            QUESTION

            Disable Check Button in Buefy Steps after clicking the check button once and proceeding to next step
            Asked 2020-Sep-28 at 06:24

            I wanted to disable the check button after it click once and proceeding to next step. I try some other ways like adding the condition in methods but it doesn't work. can anyone guide me? Thank you.

            Here is my code:

            https://codesandbox.io/s/angry-rosalind-c2dxd?file=/src/App.vue

            ...

            ANSWER

            Answered 2020-Sep-28 at 06:24
            
              
                
                  
                    
                    
            
                    
                    
            
                    
                    
            
                    
                      Finish
                      Lorem ipsum dolor sit amet.
                    
            
                    
                      
                        

            Check

            Source https://stackoverflow.com/questions/64096405

            QUESTION

            Python: Rosalind Consensus and Profile
            Asked 2020-Apr-19 at 08:51

            I am trying to solve the "Consensus and Profile" challenge on Rosalind. The challenge instructions are as follows:

            Given: A collection of at most 10 DNA strings of equal length (at most 1 kbp) in FASTA format.

            Return: A consensus string and profile matrix for the collection. (If several possible consensus strings exist, then you may return any one of them.)

            My code is as follows (I got most of it from another user on this website). My only issue is that some of the DNA strands are broken down into multiple separate lines, so they are being appended to the "allstrings" list as separate strings. I am trying to figure out how to write each consecutive line that does not contain ">" as a single string.

            ...

            ANSWER

            Answered 2020-Apr-18 at 10:37

            There are a couple of ways that you can iterate a FASTA file as records. You can use a prebuilt library or write your own.

            A widely used library for working with sequence data is biopython. This code snippet will create a list of strings.

            Source https://stackoverflow.com/questions/61278530

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

            Vulnerabilities

            No vulnerabilities reported

            Install Rosalind

            You can download it from GitHub.
            You can use Rosalind 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 .
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            https://github.com/cdeterman/Rosalind.git

          • CLI

            gh repo clone cdeterman/Rosalind

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            git@github.com:cdeterman/Rosalind.git

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