primers | A PCR primer tool for DNA assembly flows | Genomics library

 by   Lattice-Automation Python Version: 0.5.10 License: MIT

kandi X-RAY | primers Summary

kandi X-RAY | primers Summary

primers is a Python library typically used in Artificial Intelligence, Genomics applications. primers 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 primers' or download it from GitHub, PyPI.

This is a tool for creating PCR primers. It has an emphasis on DNA assembly and makes it easy to add sequences to the end of PCR fragments. This is part of overlap extension polymerase chain reaction and preparing unstandardized DNA sequences for Gibson assembly and Golden gate cloning. primers quickly creates pairs with optimized lengths, Tms, GC ratios, secondary structures (minimum free energies) and without off-target binding sites. Each returned primer has two tms: "tm", the melting temperature for the portion of the primer that binds to the template sequence, and "tm_total", the melting temperature for the entire primer with additional sequence added to its 5' end. Unlike the most used alternative, Primer3, primers has a permissive MIT license and support for adding sequence to the 5' ends of primers.
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    Quality
      Security
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            kandi-support Support

              primers has a low active ecosystem.
              It has 5 star(s) with 0 fork(s). There are 5 watchers for this library.
              There were 6 major release(s) in the last 12 months.
              There are 0 open issues and 1 have been closed. On average issues are closed in 1 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of primers is 0.5.10

            kandi-Quality Quality

              primers has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              primers 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

              primers releases are not available. You will need to build from source code and install.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed primers and discovered the below as its top functions. This is intended to give you an instant insight into primers implemented functionality, and help decide if they suit your requirements.
            • Run the program
            • Generates primers for a sequence
            • Parse command line arguments
            • Creates a pair of primers from fwd_primers
            • Returns a list of primers for a given sequence
            • Build a Primer
            • Parse the add command line
            • Takes a sequence and returns a list of mutated sites
            • Parse seq and check sequence
            • Builds a two - dimensional pair
            • Return the reverse of a sequence
            Get all kandi verified functions for this library.

            primers Key Features

            No Key Features are available at this moment for primers.

            primers Examples and Code Snippets

            primers,Usage,CLI
            Pythondot img1Lines of Code : 31dot img1License : Permissive (MIT)
            copy iconCopy
            $ primers AATGAGACAATAGCACACACAGCTAGGTCAGCATACGAAA -f GGTCTC -r GAAGAC
              dir    tm   ttm     dg   pen  seq
              FWD  62.4  68.6  -1.86  5.43  GGTCTCAATGAGACAATAGCACACACA
              REV  62.8  67.4      0   4.8  GAAGACTTTCGTATGCTGACCTAG
            
            $ primers --help
            usage: p  
            primers,Algorithm,Scoring
            Pythondot img2Lines of Code : 16dot img2License : Permissive (MIT)
            copy iconCopy
            PENALTY(p) =
                abs(p.tm - opt_tm) * penalty_tm +   // tm diff
                abs(p.gc - opt_gc) * penalty_gc +   // GC ratio diff
                abs(len(p) - opt_len) * penalty_len +      // length diff
                abs(p.tm - p.pair.tm) * penalty_tm_diff +  // tm diff between p  
            primers,Usage,Python
            Pythondot img3Lines of Code : 16dot img3License : Permissive (MIT)
            copy iconCopy
            from primers import primers
            
            # add enzyme recognition sequences to FWD and REV primers: BsaI, BpiI
            fwd, rev = primers("AATGAGACAATAGCACACACAGCTAGGTCAGCATACGAAA", add_fwd="GGTCTC", add_rev="GAAGAC")
            print(fwd.fwd)  # True
            print(fwd.seq)  # GGTCTCAATGA  

            Community Discussions

            QUESTION

            TypeError: Cannot read property 'app' of undefined Error - Flutter using firebase Auth and Firestore in flutter web app
            Asked 2021-Jun-07 at 12:44
             Running with sound null safety 
            TypeError: Cannot read property 'app' of undefined
                at Object.app$ [as app] (http://localhost:49841/packages/firebase_core_web/src/interop/core.dart.lib.js:42:101)
                at new cloud_firestore_web.FirebaseFirestoreWeb.new (http://localhost:49841/packages/cloud_firestore_web/src/write_batch_web.dart.lib.js:988:64)
                at Function.registerWith (http://localhost:49841/packages/cloud_firestore_web/src/write_batch_web.dart.lib.js:842:73)
                at Object.registerPlugins (http://localhost:49841/packages/nse7a/generated_plugin_registrant.dart.lib.js:33:46)
                at main (http://localhost:49841/web_entrypoint.dart.lib.js:41:35)
                at main.next ()
                at runBody (http://localhost:49841/dart_sdk.js:37229:34)
                at Object._async [as async] (http://localhost:49841/dart_sdk.js:37260:7)
                at main$ (http://localhost:49841/web_entrypoint.dart.lib.js:40:18)
                at http://localhost:49841/main_module.bootstrap.js:19:10
                at Array.forEach ()
                at window.$dartRunMain (http://localhost:49841/main_module.bootstrap.js:18:32)
                at :1:8
                at Object.runMain (http://localhost:49841/dwds/src/injected/client.js:8656:21)
                at http://localhost:49841/dwds/src/injected/client.js:22068:19
                at _wrapJsFunctionForAsync_closure.$protected (http://localhost:49841/dwds/src/injected/client.js:3830:15)
                at _wrapJsFunctionForAsync_closure.call$2 (http://localhost:49841/dwds/src/injected/client.js:10905:12)
                at Object._asyncStartSync (http://localhost:49841/dwds/src/injected/client.js:3794:20)
                at main__closure1.$call$body$main__closure (http://localhost:49841/dwds/src/injected/client.js:22080:16)
                at main__closure1.call$1 (http://localhost:49841/dwds/src/injected/client.js:22007:19)
                at StaticClosure._rootRunUnary [as call$2$5] (http://localhost:49841/dwds/src/injected/client.js:4153:16)
                at _CustomZone.runUnary$2$2 (http://localhost:49841/dwds/src/injected/client.js:12136:39)
                at _CustomZone.runUnaryGuarded$1$2 (http://localhost:49841/dwds/src/injected/client.js:12068:14)
                at _ControllerSubscription._sendData$1 (http://localhost:49841/dwds/src/injected/client.js:11697:19)
                at _DelayedData.perform$1 (http://localhost:49841/dwds/src/injected/client.js:11849:59)
                at _PendingEvents_schedule_closure.call$0 (http://localhost:49841/dwds/src/injected/client.js:11898:14)
                at Object._microtaskLoop (http://localhost:49841/dwds/src/injected/client.js:3990:24)
                at StaticClosure._startMicrotaskLoop (http://localhost:49841/dwds/src/injected/client.js:3996:11)
                at _AsyncRun__initializeScheduleImmediate_internalCallback.call$1 (http://localhost:49841/dwds/src/injected/client.js:10774:9)
                at invokeClosure (http://localhost:49841/dwds/src/injected/client.js:1250:26)
                at MutationObserver. (http://localhost:49841/dwds/src/injected/client.js:1269:18)
            ERROR - 2021-03-28 17:45:59.793377
            GET /web_entrypoint.dart.lib.js:40:18
            Error thrown by handler.
            FormatException: Illegal scheme character (at character 4)
            web_entrypoint.dart.lib.js:40:18
               ^
            
            dart:core                                                 _Uri.resolve
            package:flutter_tools/src/isolated/devfs_web.dart 503:57  WebAssetServer._resolveDartFile
            package:flutter_tools/src/isolated/devfs_web.dart 395:17  WebAssetServer.handleRequest
            package:dwds/src/handlers/injector.dart 110:32            DwdsInjector.middleware..
            
            
            ...

            ANSWER

            Answered 2021-Mar-28 at 19:01

            I'll try to break it up as much as possible, but there are plenty of things to be done.

            • As per the documentation, when working with Flutter Web and Firebase, you need to add your Firebase dependencies in your index.html, like this:

            Use the dependencies that you want, but if you aren't using analytics, leave it out. You have to import this first thing though firebasejs/8.3.0/firebase-app.js

            Source https://stackoverflow.com/questions/66843752

            QUESTION

            Firebase Deploy - Flutter web - Uncaught TypeError: Cannot read property 'isSupported' of undefined / Failed to register a ServiceWorker for scope
            Asked 2021-May-17 at 21:06

            My Flutter web app provides 2 error messages after deploying to firebase. The error messages were not appearing prior deployment. I can not find the root cause.

            ...

            ANSWER

            Answered 2021-May-17 at 21:06

            I found the solution

            1. I removed the following

              if ('serviceWorker' in navigator) { window.addEventListener('load', function () { navigator.serviceWorker.register('flutter_service_worker.js'); }); }
            2. I upgraded all the javascript links and launched again Firebase Initiates.

            Source https://stackoverflow.com/questions/67555420

            QUESTION

            Flutter Web - Firebase: No Firebase App '[DEFAULT]' has been created - call Firebase App.initializeApp() (app/no-app)
            Asked 2021-Apr-18 at 17:24

            I have this error emessage No Firebase App '[DEFAULT]' has been created when I try to run the Flutter Web version, Chrome is blank after running the web app.

            All my dependencies are uptodate. firebase_analytics: ^7.0.0 firebase_auth: ^1.0.0 firebase_storage: ^8.0.0 cloud_firestore: ^1.0.4

            I added firebase.initializeApp()on Main.dart, I followed the guide No Firebase App '[DEFAULT]' has been created - call Firebase.initializeApp() in Flutter and Firebase

            ...

            ANSWER

            Answered 2021-Apr-18 at 17:24

            Please add your firebase web config file to your index.html

            Ex:

            Source https://stackoverflow.com/questions/67151417

            QUESTION

            Can't read data from Firestore from Flutter Web (works on iOS and android)
            Asked 2021-Mar-31 at 22:23

            In my application I can log in (using firebase auth) on both iOS, android and web. When I try reading from Firestore database using a streambuilder, then it only works in iOS and android. In the web-part it goes straight to the else-clause of snaps.HasData.

            My index.html-file (firebaseConfig removed obviously):

            ...

            ANSWER

            Answered 2021-Mar-31 at 22:23

            Found a solution here Stackoverflow: Flutter Web - Fetching Firestore collection

            Apparently using version 8.3.0 was the problem. Use 7.14.4 instead

            Source https://stackoverflow.com/questions/66671709

            QUESTION

            Vectorize function acting on indexes
            Asked 2021-Jan-18 at 02:08

            TL;DR: I understand that .apply() is slow in pandas. However, I have a function that acts on indexes, which I cannot figure out how to vectorize. I want this function to act on two sets of parameters (500,000 and 1,500 long, respectively). I want to produce a dataframe with the first parameter as the row index, the second parameter as column names, and the cells containing the function's output for that particular row and column. As it stands it looks like the code will take several days to run. More details and minimal reproducible example below:

            INPUT DATA:

            I have a series of unique student IDs, which is 500,000 students long. I have a df (exam_score_df) that is indexed by these student IDs, containing each student's corresponding scores in math, language, history, and science.

            I also have a series of school codes (each school code corresponds to a school), which is 1,500 schools long. I have a df (school_weight_df) that is indexed by school codes, containing the school's weights in math, language, history, and science that it uses to calculate a student's scores. Each row also contains a 'Y' or 'N' indexed 'Alternative_Score' because some schools allow you to take the best subject score between history and science to calculate your overall score.

            FUNCTION I WROTE TO BE VECTORIZED:

            ...

            ANSWER

            Answered 2021-Jan-18 at 02:08

            Apply = bad, Double Apply = very bad

            If you are going Numpy in the function, why not go Numpy all the way? You would still prefer a batch-wise approach since the overall matrix would take tons of memory. Check the following approach.

            Each iteration took me 2.05 seconds on a batch of 5000 students on a low-end macbook pro. This means for 500,000 students, you can expect 200 seconds approx, which is not half bad.

            I ran the following on 100000 students and 1500 schools which took me a total of 30-40 seconds approx.

            1. First I created a dummy set data: Exam scores (100,000 students, 4 scores), school weights (1500 schools, 4 weights) AND a boolean flag for which school has alternative as Y or N, Y==True, N==False

            2. Next, for a batch of 5000 students, I simply calculate the element-wise product of each of the 4 subjects between the 2 matrices using np.einsum. This gives me (5000,4) * (1500,4) -> (1500,5000,4). Consider this as the first part of the dot product (without the sum).

            3. The reason I do this is because this is a necessary step for both your conditions N or Y.

            4. Next, FOR N: I simply filter the above matrix based on alt_flag, reduce it (sum) over last axis and transpose to get (5000, 766), where 766 are the number of schools with alternative == N

            5. FOR Y:, I filter based on alt_flag and then I calculate the sum of the first 2 subjects (because they are common) and add those to the 3rd and 4th subject separately, take a max and return that as my final score. Post that a Transpose. This gives me (5000, 734).

            6. I do this for each batch of 5000, until I have appended all the batches and then simply np.vstack to get the final tables (100000, 766) and (100000, 734).

            7. Now I can simply stack these over axis=0 to get (100000, 1500) but if I want to map them to the IDs (student, schools), it would be easier to do it separately using pd.DataFrame(data, columns=list_of_schools_alt_Y, index=list_of_student_ids and then combine them. Read the last step for you.

            8. Last step is for you to perform since I don't have the complete dataset. Since the order of the indexes is retained through batch-wise vectorization, you can now simply map the 766 school IDs with N, 734 school IDs with Y, and 100000 student IDs, in the order they occur in your main dataset. Then simply append the 2 data frames to create a final (massive) dataframe.

            9. NOTE: you will have to change the 100000 to 500000 in the for loop, don't forget!!

            Source https://stackoverflow.com/questions/65767012

            QUESTION

            Flutter Web pass Firebase Auth to HTML
            Asked 2020-Dec-20 at 17:16

            On a Flutter Web Application, I initialize Firebase in the index.html like below.

            ...

            ANSWER

            Answered 2020-Dec-20 at 17:16

            There is no way to pass a FirebaseApp instance (or services taken from that such as the database or auth) between pages. Each web page that loads in a browser is its own instance, and will need to load the Firebase services it uses.

            Source https://stackoverflow.com/questions/65382494

            QUESTION

            Why service worker restarts only on second load?
            Asked 2020-Dec-07 at 15:56

            In this docs, I found this snippet:

            After the activation step, the service worker will control all pages that fall under its scope, though the page that registered the service worker for the first time won't be controlled until it's loaded again.

            I don't think I quite understand this sentence. For me, it seems to mean that:

            • When the user requests a page, the browser always checks for new service worker (bypassing any cache).
            • If a new service worker is present - install it and activate it.
            • Wait for the user to reload the page for the new service worker to take charge.

            It doesn't make sense to me. Why make a new service worker take charge only when the user restarts the page, why not make him a primary service worker right away?

            ...

            ANSWER

            Answered 2020-Dec-07 at 15:56

            Because of consistency as explained in https://developers.google.com/web/fundamentals/primers/service-workers/lifecycle#activate I interpret it as : your user may be filling a form. You don't want the page to change behavior in the middle of his action.

            Source https://stackoverflow.com/questions/65142300

            QUESTION

            Running flutter web app locally without android studio throws firebase error
            Asked 2020-Nov-27 at 20:45

            After the successful installation of my flutter web app in a local server (following this answer by using express) I'm able to run my flutter app on localhost. However, upon accessing it, the console displays the error

            main.dart.js:28998 Uncaught ReferenceError: firebase is not defined

            I presume that I need to install and reference firebase in my app.js but I actually have no idea how it's done (if this is actually the case). I tried running the command npm install firebase which seems to successfully install it however I'm still getting this error.

            Do you know what I might be missing or why I am getting this error and how to solve it?

            Note that the project works perfectly if ran on Chrome when built using Android Studio so it must be something to do with the local hosting.

            Edit

            This is my current index.html which is working perfectly when I run the project through Android Studio on Chrome

            ...

            ANSWER

            Answered 2020-Nov-27 at 20:45

            Make sure to include the overall firebase script and the services you're using in your index.html in the web folder. Do it before the line in the body.

            Note that even if flutter works well with the index.html as you have it, it's likely that this is the reason why it's not working on your local server.

            In your case, move all the firebase related scripts (including the configuration script) before the main.dart.js script:

            Source https://stackoverflow.com/questions/65042247

            QUESTION

            Split phrase in n characters completing whole words in Notepad++
            Asked 2020-Nov-16 at 15:01

            I've a .txt like this:

            ...

            ANSWER

            Answered 2020-Nov-16 at 15:01

            You need to add a stop once you find the first space ^SN .{220}[^\s]*, no sure if it is necessary but you can also add "or" (|) for ponctuation.

            Source https://stackoverflow.com/questions/64860202

            QUESTION

            Flutter Web : javascript Uncaught ReferenceError: Firebase is not defined?
            Asked 2020-Nov-11 at 08:43

            I am trying to add firebase to my flutter web app, i keep getting this error and i dont know why anymore, i have tried everything

            Google chrome console error

            ...

            ANSWER

            Answered 2020-Nov-11 at 08:43

            I would love to help you but could you share the error you get in the Chrome console log?

            Usually, the problem is that you are using firestore and others but did not include them in the index.html.

            For example:

            Source https://stackoverflow.com/questions/64782788

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

            Vulnerabilities

            No vulnerabilities reported

            Install primers

            You can install using 'pip install primers' or download it from GitHub, PyPI.
            You can use primers 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 .
            Find more information at:

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            Install
          • PyPI

            pip install primers

          • CLONE
          • HTTPS

            https://github.com/Lattice-Automation/primers.git

          • CLI

            gh repo clone Lattice-Automation/primers

          • sshUrl

            git@github.com:Lattice-Automation/primers.git

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