primers | A PCR primer tool for DNA assembly flows | Genomics library
kandi X-RAY | primers Summary
kandi X-RAY | primers Summary
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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Top functions reviewed by kandi - BETA
- 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
primers Key Features
primers Examples and Code Snippets
$ 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
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
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
Trending Discussions on primers
QUESTION
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 19:01I'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
QUESTION
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 21:06I found the solution
I removed the following
if ('serviceWorker' in navigator) { window.addEventListener('load', function () { navigator.serviceWorker.register('flutter_service_worker.js'); }); }I upgraded all the javascript links and launched again Firebase Initiates.
QUESTION
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 17:24Please add your firebase web config file to your index.html
Ex:
QUESTION
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 22:23Found a solution here Stackoverflow: Flutter Web - Fetching Firestore collection
Apparently using version 8.3.0 was the problem. Use 7.14.4 instead
QUESTION
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 02:08Apply = 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.
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
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).The reason I do this is because this is a necessary step for both your conditions N or Y.
Next,
FOR N:
I simply filter the above matrix based onalt_flag
, reduce it (sum) over last axis and transpose to get(5000, 766)
, where 766 are the number of schools withalternative == N
FOR Y:
, I filter based onalt_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)
.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)
.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 usingpd.DataFrame(data, columns=list_of_schools_alt_Y, index=list_of_student_ids
and then combine them. Read the last step for you.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.
NOTE: you will have to change the 100000 to 500000 in the for loop, don't forget!!
QUESTION
On a Flutter Web Application, I initialize Firebase in the index.html like below.
...ANSWER
Answered 2020-Dec-20 at 17:16There 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.
QUESTION
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 15:56Because 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.
QUESTION
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 20:45Make 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:
QUESTION
I've a .txt like this:
...ANSWER
Answered 2020-Nov-16 at 15:01You 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.
QUESTION
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 08:43I 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:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install primers
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.
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