sketchy | Genomic neighbor typing of bacterial pathogens using MinHash | Genomics library
kandi X-RAY | sketchy Summary
kandi X-RAY | sketchy Summary
Sketchy is a lineage calling and genotyping tool based on the heuristic principle of genomic neighbor typing developed by Karel Břinda and colleagues (2020). It queries species-wide ('hypothesis-agnostic') reference sketches using MinHash and infers associated genotypes based on the closest match, including multi-locus sequence types, susceptibility profiles, virulence factors or other genome-associated features provided by the user. Unlike the original implementation in RASE, Sketchy does not use phylogenetic trees which has some downsides, e.g. for sublineage genotype predictions (see below). See the latest docs for install, usage and database building.
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Top functions reviewed by kandi - BETA
- Parse metadata from a JSON file .
- Process reference data .
- Compute metrics from reference and prediction .
- Clean metadata from a metadata file .
- Get metrics from reference prediction .
- Read label config file .
- Command line options .
- Compute the metrics for binary classification .
- Calculate the metric .
sketchy Key Features
sketchy Examples and Code Snippets
Community Discussions
Trending Discussions on sketchy
QUESTION
Context: adding a new resource to TF Provider
After I read HashiCorp's tutorial about Retries and Customizable Timeouts and figuring out the creation (that uses StateChangeConf) might take more than default 20 minutes for Create operation I set a custom timeout for a resource:
ANSWER
Answered 2022-Apr-10 at 09:20Disclaimer :: By no means, I'm a golang expert but I think I've some understanding on this.
I've checked our tfstate files based on azurerm provider & indeed found "timeouts": null on various resources.
However, having gone through the issue mentioned here, null is indeed expected here. Explanation provided by hashicorp team is below..
The "timeouts" field in the state is only representative of the configuration values. Terraform core isn't aware of the default values, as those are looked up at runtime by the provider SDK. The provider SDK does encode the timeouts into the "private" field for later reference however. There was an issue with delete timeout values being lost at one point, but that should only show up with an old AWS provider as it's been fixed for a few months.
That means, we should be looking at the field private rather timeouts. In fact, our state file had "private": "eyJlMmJmYjczMC1lY2FhLTExZTYtOGY4OC0zNDM2M2JjN2M0YzAiOnsiY3JlYXRlIjoxODAwMDAwMDAwMDAwLCJkZWxldGUiOjE4MDAwMDAwMDAwMDAsInJlYWQiOjMwMDAwMDAwMDAwMCwidXBkYXRlIjoxODAwMDAwMDAwMDAwfX0=",. It's base64 encoded.
When I decode, I see below output.
QUESTION
I am currently trying to implement a hashrouter and Im getting the error: No routes matched location "register" going to the url localhost:3000/#register
My index.js:
...ANSWER
Answered 2022-Mar-21 at 20:18The links in NavDom should be react-router-dom links and they should link to pages the app is rendering. The URL will end up something like localhost:3000/#/register.
QUESTION
As part of a custom Encoder, I am coding an UnkeyedEncodingContainer. However, the specific format I am making it for asks that all elements of an array be of the same type. Specifically, arrays can contain :
- Integers one same size
- Floats or Doubles
- Other arrays (not necessarily all containing the same kinds of elements)
- Objects
Here is the type of answer I need : The basis of an
UnkeyedEncodingContainerimplementation that conforms to the protocol, and enforces that all elements be of one same type among the above specified ones.
As requested, here are examples of things that should or should not be encodable :
...ANSWER
Answered 2022-Mar-16 at 10:10Unless anyone has a better idea, here is the best I could come up with :
- Do not enforce that all elements be of the same type inside the
UnkeyedEncodingContainer - If all elements are the same type, encode it as an array
- If elements have varying types, encode it as a dictionary with integers as keys
This is completely fine as far as the encoding format goes, has minimal costs and only slightly complicates decoding (check whether keys contain integers) and greatly widens how many different Swift object will be compatible with the format.
Note : Remember that the "real" encoding step where the data is generated is not actually part of the protocol. That is where I am proposing the shenanigans should take place 😈
QUESTION
I have wracked my brain trying to come up with a solution to this problem and I'm at wits end! First, the necessary context: Aquatic plants in lakes are sampled with rakes. You throw a rake out into the lake, you pull it back into your boat, and you figure out what plants are on its tines. In our case, we measure both presence/absence as well as "abundance," but in an ordinal/interval-censored way --> it's 0 if species X isn't noticed on the rake at all, 1 if it covers < 25% of the rake's tines, 2 if it covers between 25 and 75%, and 3 if it covers > 75%. However, it's fairly easy to miss a species entirely when it's in low abundance, so 0s are sketchy--they may not represent true absences, and that is really the issue our model is trying to explore.
So, there are really three layers here--a true, fully latent abundance that we don't observe directly at all, a partially latent "true presence/absence" in that we know where true presences are but not where true absences are, and then we have our observed presence/absence data. What's more interesting is that we think some environmental variables may affect both true abundance and true occurrence but differently, and then other variables may affect detectability, and it's those processes we're trying to tease apart.
So, anyhow, my actual model is much larger and more complicated than what I've pasted below, but here is a sort of functional (but probably academically meritless) training version of it that replicates the error I am getting.
...ANSWER
Answered 2022-Feb-21 at 10:45I have run your example with JAGS 4.3.0 and rjags 4-12. For me, the version with rjags runs correctly. The version with runjags does not work because you have not provided intial values. This is easily fixed by adding the argument
QUESTION
There are a couple of notable packages on pub.dev that offer video compression. I've tried them, and other sketchy packages, and none work well once a video gets around 300MB. They crash or have other issues on various platforms and hardware. Namely, video compress and light compressor. The GH commits and support are concerning as well on the packages I've seen for video compression in pub.dev. PR's not being pulled in and issues not being resolved in a timely manner and some quite serious for recent android APK updates. So not something I want in my dependency stack.
I am uploading to Google Cloud Storage using FlutterFire. While my code does upload using FireBaseStorage upload task it does not have any ability to compress on the client side or handle background uploading when the app is closed.
So, currently on the server side, I have a GCF that triggers on file uploaded. Then I use nodejs ffmpeg, which is baked into GCF's to compress server side and convert to H264. And finally delete the original large upload video and save the compressed video to storage.
This solution works, but depending on a user's connection and whether they are on wifi, can take an awful long time and when it fails or the user closes the app, my current solution is useless.
I wish there was a solid native library on Android and iOS, that I could tap into, to confidently perform compression and conversion from any format to H264 and also allow uploading, whether my app is closed or in the background, to GC storage. Any thoughts? I wish this was standard in FlutterFire's cloud storage handling!
I have yet to test flutter_ffmpeg, but only because some have said it runs so slowly on client. So again, Flutter/Dart can access natively written code, but I don't know where to start on Android/iOS to do this the right way. And I understand this is what some of the packages are doing, but they do not work with large videos, so I'm hoping someone can point me in the right direction on Android and iOS.
My code for handling upload tasks to GC storage.
...ANSWER
Answered 2022-Feb-20 at 03:41I did resolve, to some degree, my original post's questions and frustrations by using the ffmpeg_kit_flutter_full_gpl package on the client side, and then ffmpeg again in GCF on the server side. In summary:
- Within 60 seconds, I can now compress a 2 minute video by 90% before uploading to firebase storage.
- Using
onFinalizevia GCF on the server side I run ffmpeg again on the uploaded video and gain another 77% reduction in file size on the server side without any loss in video quality. - My solution does not yet upload while the app is closed.
- On the client side, this solution requires setting the camera
ResolutionPresettohigh(720p), rather thanmax, which can be a minimum of 1080p, and setting the ffmpeg-preset veryfastrather than themediumdefault.
Camera & ffmpeg solution settings:
- Flutter camera package
ResolutionPresettohigh - ffmpeg
-preset veryfast
Transcoding results stats for 2 minute video:
- Before transcode: 255MB
- After client side transcode: 25MB (90% decrease in size before upload)
- Time to transcode: 60 seconds
onFinalizedGCF ffmpeg transcode: 19MB (77% reduction in size)- In total a 93% reduction in size while keep high quality 720p video.
flutter_ffmpeg is archived, the new ffmpeg flutter package is ffmpeg_kit_flutter.
That being said, I used ffmpeg_kit_flutter to build my solution on the client side, rather than the server side, and transcode the video before uploading.
Cons:
- Doubled my app size to use ffmpeg, because I needed access to both
lameandx264so I had to install the full-gpl package to gain access to these libraries. - A two minute video can take up to 60 seconds to transcode.
The pros:
- Low bandwidth connections will operate much better after a video is reduced in size by 90%.
- Large videos will transcode and ffmpegkit does not crash like other flutter packages I've tried.
- The second pass with ffmpeg on GCF gains another 77% reduction in size taking a video of 100's of MB's down to just 10-20 MB max for eventually delivery.
- Costs lower on the front and back end.
So, you'll have to decide if the pros outweighs the cons and if 720p is high enough quality for playback. For me 720p looks perfect for video playback on a mobile phone and 1080p or higher was big time overkill.
I've provided sample code (not full classes) to give anyone looking to implement my solution a try. It became very important, due to the amount of time to transcode, to display a progress meter so the user does not give up on the process. You'll see my simple solution to displaying transcoding progress.
pubspec.yaml
- camera package for video recording
- riverpod required for statenotifier and transcode/upload progress notifications
- ffmpeg_kit_flutter_full_gpl (the full_gpl gets the ffmpeg package with most libraries) required to get
h264andlibmp3lameencoders to produce most widely playable transcoded videos. - wakelock required because transcoding takes so long you don't want the phone to sleep while transcoding.
QUESTION
I'm trying to toggle between a moon icon and a sun icon on a dark mode project. The original javascript code was simply a button that switched from day mode to dark mode. After some research, I ended up with the following code, which "kinda" works but is sketchy; it switches from day mode to dark mode and the icon toggles from moon to sun BUT, when I come back to the page after setting my preference as dark mode (or refreshing the page in dark mode), the icon disappears.
...ANSWER
Answered 2022-Feb-13 at 03:43You need to toggle both classes each time you want to make a switch.
Your code was using the toggle method as though it would swap moon for sun but it really just toggles whether the individual class is there. I've toggled both classes when we need to make a change, and commented out the local storage stuff to avoid JS errors with the SO snippet, but otherwise didn't change your code.
QUESTION
Long time user, first time poster. :-)
I'm using discord.py==1.7.2. I have a probably complicated bot that I have been hacking out through trial and error (super sketchy documentation as far as I can tell and maybe I don't really understand the Discord concept), but I am seeing some super strange behavior in the on_message() event. After having everything working like I wanted, I noticed an issue and simply wanted to check a value when the on_message() event was executed. I printed it to the chat. I then noticed it was printed repeatedly, non-stop to the chat until I killed the bot. Am I missing something here? My expectation is that the event on_message() runs when a user enters something and presses enter and then stops. Is this wrong? Code:
...ANSWER
Answered 2022-Feb-06 at 00:09This is because your event is on_message, and you are sending a message inside this event, which then triggers the event again, and then sends a message again and so on, in a loop.
you should check the sender of the message, if its the bot, then return. like so,
QUESTION
I have transcriptions of speech with "mirror-image" delimiters, i.e., paired symbols marking opening and, respectively, closing, such as ( and ) or < and >. The delimiter in this data is the square bracket:
ANSWER
Answered 2022-Jan-22 at 19:21May use the pattern (\\[[^\\]]+(\\[|$)|(^|\\])[^\\[]+\\]) in str_detect
QUESTION
I want to change my account leverage on FTX with there rest API. Just for a test because after that I want to post an order. But I cant get both of them working and for some reason I cant figure out how to do it.
So far I am able to do a get request and the authentication for it. This is the code I use for such an get request WITH authentication. I use PHP to do it and use Javascript to fetch the php file.
...ANSWER
Answered 2022-Jan-21 at 07:10I figured out how to do it. It had to do with the $parameters and @signature. When doing a POST request you need to json_encode() the parameters and then use it in the $signature. See $specialParam. Below code makes it possible to chance leverage.
QUESTION
Suppose I want to run the following C snippet:
...ANSWER
Answered 2022-Jan-07 at 13:57but what is the purpose of scanf then?
An excellent question.
Is it simply an useless broken function that should never be used?
It is almost useless. It is, arguably, quite broken. It should almost never be used.
Why is it in the libraries to begin with then?
My personal belief is that it was an experiment. It tries to be the opposite of printf. But that turned out not to be such a good idea in practice, and the function never got used very much, and pretty much fell out of favor, except for one particular use case...
This seems really absurd, especially considering all beginners are taught to use scanf...
You're absolutely right. It is really quite absurd.
There's a reason all beginners are taught to use scanf. During week 1 of your first C programming class, you might write the little program
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Install sketchy
Rust is installed and managed by the rustup tool. Rust has a 6-week rapid release process and supports a great number of platforms, so there are many builds of Rust available at any time. Please refer rust-lang.org for more information.
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