PropagAtE | Prophage Activity Estimator
kandi X-RAY | PropagAtE Summary
kandi X-RAY | PropagAtE Summary
If you find PropagAtE useful please consider citing our preprint in bioRxiv: Kieft, K., and Anantharaman, K. (2021). Deciphering active prophages from metagenomes. BioRxiv 2021.01.29.428894.
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Top functions reviewed by kandi - BETA
- Extract coverage
- Calculate the CohenD distribution
- Compute coverage stats for each scaffold
- Add a read depth
- Compute host stats for a given depth
- Add a depth to the depth list
- Compute statistics for host coverage
- Include zeros
- Write a coverage file
- Calculate the activity of a given ratio
- Return a dictionary mapping positions and positions
- Reverse start and stop
- Get the length between start and stop
- Build bowtie2
- Parse fasta file
- Setup setup
- Extract the length of each genome
- Returns the contents of the README md file
- Return the version string
PropagAtE Key Features
PropagAtE Examples and Code Snippets
Lines of Code : 15License : Non-SPDX (Apache License 2.0)
Copydef maybe_propagate_compile_time_consts_in_xla(op):
"""Tells XLA whether to propagate compile-time consts in the loop body.
This is needed to make compile time constants available to ops, for example
`max_num_elements` in `EmptyTensorList`, in public static void propagateException() throws InterruptedException {
Thread.sleep(1000);
Thread.currentThread().interrupt();
if (Thread.interrupted()) {
throw new InterruptedException();
}
} def _propagate(self, idx, change):
parent = (idx - 1) // 2
self.tree[parent] += change
if parent != 0:
self._propagate(parent, change) Community Discussions
Trending Discussions on PropagAtE
QUESTION
This question is about two MAUI controls (Switch and ListView) - I'm asking about them both in the same question as I'm expecting the root cause of the problem to be the same for both controls. It's entirely possible that they're different problems that just share some common symptoms though. (CollectionView has similar issues, but other confounding factors that make it trickier to demonstrate.)
I'm using 2-way data binding in my MAUI app: changes to the data can either come directly from the user, or from a background polling task that checks whether the canonical data has been changed elsewhere. The problem I'm facing is that changes to the view model are not visually propagated to the Switch.IsToggled and ListView.SelectedItem properties, even though the controls do raise events showing that they've "noticed" the property changes. Other controls (e.g. Label and Checkbox) are visually updated, indicating that the view model notification is working fine and the UI itself is generally healthy.
Build environment: Visual Studio 2022 17.2.0 preview 2.1
App environment: Android, either emulator "Pixel 5 - API 30" or a real Pixel 6
The sample code is all below, but the fundamental question is whether this a bug somewhere in my code (do I need to "tell" the controls to update themselves for some reason?) or possibly a bug in MAUI (in which case I should presumably report it)?
Sample codeThe sample code below can be added directly a "File new project" MAUI app (with a name of "MauiPlayground" to use the same namespaces), or it's all available from my demo code repo. Each example is independent of the other - you can try just one. (Then update App.cs to set MainPage to the right example.)
Both examples have a very simple situation: a control with two-way binding to a view-model, and a button that updates the view-model property (to simulate "the data has been modified elsewhere" in the real app). In both cases, the control remains unchanged visually.
Note that I've specified {Binding ..., Mode=TwoWay} in both cases, even though that's the default for those properties, just to be super-clear that that isn't the problem.
The ViewModelBase code is shared by both examples, and is simply a convenient way of raising INotifyPropertyChanged.PropertyChanged without any extra dependencies:
ViewModelBase.cs:
...ANSWER
Answered 2022-Apr-09 at 18:07These both may be bugs with the currently released version of MAUI.
This bug was recently posted and there is already a fix for the Switch to address this issue.
QUESTION
Everytime I open a new session in RStudio, I'm greeted with the error message:
...ANSWER
Answered 2022-Mar-28 at 19:26Your user .Rprofile file is loading itself recursively for some reason:
QUESTION
I am working on a (Open)Modelica library for simulating chemical processes. With commercial tools it is a common approach that the mixture configuration (e.g. how many and which chemical components are involved like water, ethanol, ...) is defined once for the feed-stream and then this information is propagated via the streams to all the subsequent unit operations.
Unfortunately, so far I did not manage to use the powerful modelica language to achieve this functionality. The ideal situation would be to model a "Process" like this:
...ANSWER
Answered 2022-Mar-14 at 16:09AFAIK, this is not possible with (Open)Modelica alone, but some tools have been amended with an automation capability:
Automatic propagation of fluid models through the ports is not directly possible with the Modelica 3.4 specification, but might be supported by the Modelica tool. For example, in Dymola the option Advanced.MediaPropagation=1 can be set to apply automatic propagation of media models in a circuit.
Dymola video demonstrating this: https://www.modelon.com/propagating-replaceable-medium-automatically/
The Modelica Specification issue in case you would like to see this included in the language/reopen discussion: https://github.com/modelica/ModelicaSpecification/issues/240
QUESTION
This question is exactly the same as this one, which wasn't actually answered (that code only uses one thread). My code looks like this at the moment
...ANSWER
Answered 2022-Mar-28 at 12:45Seems to work thanks to this example. The snippet above becomes:
QUESTION
I have a class with a method (getter) that performs some relatively expensive operation, so I want to cache its result. Calling the method does not change behavior of the object, but it needs to store its result in this, so it can't be const.
The problem is that I now have another method that is const and I need to invoke my getter. Is there some generally accepted solution to this problem? Should I bypass the constness checking in the getter to make it const, (Coudn't that cause problems with optimizing compiler?) or I have to propagate the non-constness to all methods that use this getter?
Example:
...ANSWER
Answered 2022-Mar-19 at 18:13This is one of the situations the mutable specifier fits particularly well. When a class member is mutable, that member can be changed even if the enclosing class is const.
So, if MyClass::cachedValue is a mutable Foo* instead of a Foo*, you can have const member functions in MyClass that make changes to cachedValue and then all calling code can just act on a const MyClass as normal.
QUESTION
How to manage access to shared resources using Project Reactor?
Given an imaginary critical component that can execute only operation at the time (file store, expensive remote service, etc), how could one orchestrate in reactive manner access to this component if there are multiple points of access to this component (multiple API methods, subscribers...)? If the resource is free to execute the operation it should execute it right away, if some other operation is already in progress, add my operation to the queue and complete my Mono once my operation is completed.
My idea is to add tasks to the flux queue which executes tasks one by one and return a Mono which will be complete once the task in the queue is completed, without blocking.
...ANSWER
Answered 2022-Feb-23 at 10:26this looks like a simplified version of what the reactor-pool does, in essence. have you considered using that with eg. a maximum size of 1?
https://github.com/reactor/reactor-pool/
https://projectreactor.io/docs/pool/0.2.7/api/reactor/pool/Pool.html
The pool is probably overkill, because it has the overhead of having to deal with multiple resources on top of multiple competing borrowers like in your case, but maybe it could provide some inspiration for you to go further.
QUESTION
I'm using Nodejs and MongoDB driver.
A two part question
- I have a collection which is called
openOfferswhich I want to expire when it hits the timecloseOfferAt. I know that MongoDB offers a TTL,expireAtandexpireAfterSeconds. But, when I use these, the same TTL is applied to all the documents in a particular collection. I'm not sure if I'm doing this correctly. I want document level custom expiry. Any syntax might be very useful! Docs inopenOffers
ANSWER
Answered 2022-Feb-22 at 02:27Do not make your application logic depend on TTL indexes.
In your app you should have some scheduler that runs periodic tasks, some of them would move the finished offers to other collection and delete from the original even in bulk and no need to set a TTL index.
To keep consistency nothing better than a single source of truth, so if you can, avoid deleting and only change some status flag and timestamps.
A good use of a TTL index is to automatically clear old data after a relative long time, like one month or more. This keeps collection/indexes size in check.
QUESTION
I have a Firebase real-time database integrated with React Native where I can create users. But my problem is that when I try to log in I get an error. I run my app on IOS if it makes any difference. I have followed this guide: How to Build a React Native App and Integrate It with Firebase. I use the method Email/Password for login. I use Firebase version 9.6.4.
I have looked through this thread: Could not reach Cloud Firestore backend. and tried all the solutions but nothing works for me.
Any suggestions on what possibly could cause the error and how do I solve it?
Error message:
[2022-01-29T10:35:40.257Z] @firebase/firestore:, Firestore (9.6.4): Could not reach Cloud Firestore backend. Connection failed 1 times. Most recent error: FirebaseError: [code=permission-denied]: Cloud Firestore API has not been used in project xxxx before or it is disabled. If you enabled this API recently, wait a few minutes for the action to propagate to our systems and retry. This typically indicates that your device does not have a healthy Internet connection at the moment. The client will operate in offline mode until it is able to successfully connect to the backend.
Firebase config.ts file:
ANSWER
Answered 2022-Feb-10 at 05:23Your error message says FirebaseError: [code=permission-denied]: Cloud Firestore API has not been used in project xxxx before or it is disabled.
The app tries to read a user document after signing in, but seems to have no access.
Check your firestore rules in your firebase console to see if read rules are valid. Firestore may have initialized with rules that allow only admin users to read/write, or rules that allow all read/write only for a month after its creation.
To make your app work, your firestore rules need to allow read access on users collection. Here are the rules you can set on your firestore. The more specific rules you set, the more secure the app is.
Allow unauthenticated access on all collections
QUESTION
I'm trying to come up with a solution to allow multiple Pane nodes handle mouse events independently when assembled into a StackPane
...ANSWER
Answered 2022-Feb-09 at 18:34Using the hint from @jewelsea I was able to use a custom chain. I've done this from a "catcher" Pane which is added to the front of the StackPane. This then builds a chain using all the children, in reverse order, excluding itself.
QUESTION
I see multiple sources claiming that an exception happening inside an async{} block is not delivered anywhere and only stored in the Deferred instance. The claim is that the exception remains "hidden" and only influences things outside at the moment where one will call await(). This is often described as one of the main differences between launch{} and async{}. Here is an example.
An uncaught exception inside the async code is stored inside the resulting Deferred and is not delivered anywhere else, it will get silently dropped unless processed
According to this claim, at least the way I understand it, the following code should not throw, since no-one is calling await:
...ANSWER
Answered 2022-Jan-29 at 10:51In some sense, the mess you experience is a consequence of Kotlin coroutines having been an early success, before they became stable. In their experimental days, one thing they lacked was structured concurrency, and a ton of web material got written about them in that state (such as your link 1 from 2017). Some of the then-valid preconceptions remained with people even after their maturation, and got perpetuated in even more recent posts.
The actual situation is quite clear — all you have to understand is coroutine hierarchy, which is mediated through the Job objects. It doesn't matter whether it's a launch or an async, or any further coroutine builder — they all behave uniformly.
With this in mind, let's go through your examples:
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You can use PropagAtE 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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