adapt | designing activity-informed nucleic acid diagnostics | Genomics library

 by   broadinstitute Python Version: v1.5.0 License: MIT

kandi X-RAY | adapt Summary

kandi X-RAY | adapt Summary

adapt is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. adapt has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install adapt' or download it from GitHub, PyPI.

The main program for designing assays is design.py.
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            kandi-support Support

              adapt has a low active ecosystem.
              It has 16 star(s) with 1 fork(s). There are 6 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 2 open issues and 8 have been closed. On average issues are closed in 171 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of adapt is v1.5.0

            kandi-Quality Quality

              adapt has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              adapt 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

              adapt releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              It has 10623 lines of code, 725 functions and 60 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed adapt and discovered the below as its top functions. This is intended to give you an instant insight into adapt implemented functionality, and help decide if they suit your requirements.
            • Prepare alignment for a single segment
            • Retrieve annotation files from refs_aligned
            • Returns the union of a list of kmer leaves
            • Extend the set of sequences from other
            • Return a list of ligos in a given interval
            • Return the weighted weight of seq_ids
            • Extract a range from positions_start to pos_end
            • Return list of sequences that are bound to the given ligand
            • Compute the predicted activity
            • Adds metadata to a list of neighbors based on metadata
            • Constructs a list of all occurrences of a given species
            • Convert argv to arguments
            • Construct a sequence of guides at each position
            • Curate a sequence of sequences against reference sequences
            • Find all guides in a sliding window with a sliding window
            • Construct a list of the neighbors of a taxid
            • Calculates the binding function for the given position
            • Reads taxonomies from a TSV file
            • Calculate the requested percentiles
            • Query a query
            • Find guides with a sliding window
            • Finds the representative sequences in a sequence of sequences
            • Finds a guide within a given window
            • Query the tree
            • Run HMC
            • Find all oligos in a window
            Get all kandi verified functions for this library.

            adapt Key Features

            No Key Features are available at this moment for adapt.

            adapt Examples and Code Snippets

            No Code Snippets are available at this moment for adapt.

            Community Discussions

            QUESTION

            Android Studio - Value must be ≥ 0
            Asked 2022-Mar-31 at 10:37

            I am getting an error in Android Studio to do with my Cursor.

            I have the following line in my code

            ...

            ANSWER

            Answered 2021-Nov-14 at 15:06

            I had an error like this.
            My solution : change method getColumnIndex into getColumnIndexOrThrow.

            Source https://stackoverflow.com/questions/69053061

            QUESTION

            The unauthenticated git protocol on port 9418 is no longer supported
            Asked 2022-Mar-27 at 13:23

            I have been using github actions for quite sometime but today my deployments started failing. Below is the error from github action logs

            ...

            ANSWER

            Answered 2022-Mar-16 at 07:01

            First, this error message is indeed expected on Jan. 11th, 2022.
            See "Improving Git protocol security on GitHub".

            January 11, 2022 Final brownout.

            This is the full brownout period where we’ll temporarily stop accepting the deprecated key and signature types, ciphers, and MACs, and the unencrypted Git protocol.
            This will help clients discover any lingering use of older keys or old URLs.

            Second, check your package.json dependencies for any git:// URL, as in this example, fixed in this PR.

            As noted by Jörg W Mittag:

            There was a 4-month warning.
            The entire Internet has been moving away from unauthenticated, unencrypted protocols for a decade, it's not like this is a huge surprise.

            Personally, I consider it less an "issue" and more "detecting unmaintained dependencies".

            Plus, this is still only the brownout period, so the protocol will only be disabled for a short period of time, allowing developers to discover the problem.

            The permanent shutdown is not until March 15th.

            For GitHub Actions:

            As in actions/checkout issue 14, you can add as a first step:

            Source https://stackoverflow.com/questions/70663523

            QUESTION

            Android Build Error: "lStar not found..."
            Asked 2022-Feb-18 at 06:59

            I have error like this after trying to build my apps in Emulator

            /Users/joel/.gradle/caches/transforms-3/06231cc1265260b25a06bafce7a4176f/transformed/core-1.7.0-alpha02/res/values/values.xml:105:5-114:25: AAPT: error: resource android:attr/lStar not found.

            I don't know what causes this error. After digging some answer which has similarly error (but in flutter) Problem. But still not solved my issue.

            I have this dependency in my project

            ...

            ANSWER

            Answered 2021-Sep-28 at 17:18

            I managed to fix this by upgrading compileSdk to 31 and kotlin gradle plugin to 1.5.10

            Source https://stackoverflow.com/questions/69041630

            QUESTION

            How do I set up NUnit in Visual Studio 2022?
            Asked 2022-Feb-01 at 20:25

            Does NUnit work under Visual Studio 2022? All of the setup instructions I can find relate to previous versions of Visual Studio and reference things that are not present (such as "Tools -> Manage Extensions menu in Visual Studio. Click on Online and enter the search term as NUnit Test Adapter" - the search yields no results). If it does work, how do I set it up?

            ...

            ANSWER

            Answered 2021-Dec-21 at 10:54

            You can add both NUnit Framework and NUnit Test Adapter using NuGet Packages.

            To do that, right click on your project in Solution Explorer, go to Manage NuGet packages..., in the Browse section type nunit, install NUnit package and the corresponding version adapter (NUnitTestAdapter for NUnit 2.x or NUnit3TestAdapter for NUnit 3.x).

            Source https://stackoverflow.com/questions/70282628

            QUESTION

            Replacing YouTube HTML links with embed code
            Asked 2022-Jan-30 at 22:33

            I'm writing web pages in markdown and converting them to HTML using md2html tool. I want to process the output HTML file and find any youtube link like this:

            https://www.youtube.com/watch?v=abcdefgh887

            and replace it with the embed code:

            I toyed around a little with Grammars, mostly to get familiar with them, but concluded this probably isn't the ideal tool for the job. Plus I'd prefer to use existing modules that are easily adaptable to other similar tasks rather than roll my own half-baked solution.

            Perl5 has some good tools for this kind of thing but I'd like to use a pure Raku solution so I can learn more Raku.

            Any recommendations for good approaches to this problem?

            ...

            ANSWER

            Answered 2022-Jan-28 at 20:31

            I tried to answer your question without knowing an example.

            You need to extract youtubeId from A tag and then replace A tag into iframe tag.

            pseudo code is:

            Source https://stackoverflow.com/questions/70899694

            QUESTION

            What is the official Rust guidance for interoperability with C++, in particular passing and returning structs as arguments?
            Asked 2022-Jan-26 at 23:08

            I'm trying to adapt some layers of existing C++ code to be used by Rust and apparently the way is through a C API.

            For example, one function might return a struct as an object

            ...

            ANSWER

            Answered 2022-Jan-21 at 01:15

            extern "C" on both sides + #[repr(C)] on the Rust side + only using C-compatible types for interfacing between C++ and Rust, should work.

            Alternatively, see cxx and autocxx.

            Source https://stackoverflow.com/questions/70794769

            QUESTION

            How to use recursion-schemes to `cata` two mutually-recursive types?
            Asked 2021-Dec-22 at 03:05

            I started with this type for leaf-valued trees with labeled nodes:

            ...

            ANSWER

            Answered 2021-Dec-18 at 17:02

            One answer to the linked question mentions adding an extra type parameter, so that instead of Tree (Labeled a) we use Tree Labeled a:

            Source https://stackoverflow.com/questions/70404315

            QUESTION

            Split a string between a word and a number
            Asked 2021-Dec-21 at 12:56

            I have some text like the following:

            ...

            ANSWER

            Answered 2021-Dec-21 at 10:12

            We can try using strsplit here as follows:

            Source https://stackoverflow.com/questions/70433678

            QUESTION

            How to write an array tag in a VARIANT structure on an OpenOPC server
            Asked 2021-Dec-07 at 16:42

            I'm trying to communicate with an OPC DA server and need to write in a tag which is in an array format. We can connect with a simulation server, read tags (int, real, array) and write tags (int, real, str). The problem comes when we need to write in an array tag. The developper of the OpenOPC library (Barry Barnreiter) recommand to use a VARIANT variable because OPC "expect to see a Windows VARIANT structure when writing complex objects such as arrays".

            • I did install Pywin32 (build 217) as suggested here.
            • I tried to send a simple integer instead of an array in a VARIANT structure.

            Here's the code:

            ...

            ANSWER

            Answered 2021-Dec-05 at 19:56

            You need to upgrade the python to 3.9 and Pywin32 to Build 302. In addition, you need to install the OpenOPC-Python3x 1.3.1.

            Source https://stackoverflow.com/questions/70118083

            QUESTION

            React Native - gradle, manifest merge error
            Asked 2021-Nov-25 at 02:04

            When trying to build my android react native app, im getting this error

            ...

            ANSWER

            Answered 2021-Nov-03 at 08:44

            For now I know that in my case it is that I have conflict between two manifest files in node_modules folder:

            Source https://stackoverflow.com/questions/69810291

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

            Vulnerabilities

            No vulnerabilities reported

            Install adapt

            It is generally useful to install and run Python packages inside of a virtual environment, especially if you have multiple versions of Python installed or use multiple packages. This can prevent problems when upgrading, conflicts between packages with different requirements, installation issues that arise from having different Python versions available, and more.

            Support

            If you have questions about ADAPT, please create an issue.
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            gh repo clone broadinstitute/adapt

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            git@github.com:broadinstitute/adapt.git

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