NEAT | NEAT project , the NExt-generation sequencing Analysis | Machine Learning library
kandi X-RAY | NEAT Summary
kandi X-RAY | NEAT Summary
Stay tuned over the coming weeks for exciting updates to NEAT, and learn how to [contribute] CONTRIBUTING.md) yourself. If you’d like to use some of our code, no problem! Just review the [license] LICENSE.md), first. NEAT-gen_reads is a fine-grained read simulator. GenReads simulates real-looking data using models learned from specific datasets. There are several supporting utilities for generating models used for simulation. This is an in-progress v3.2 of the software. For a stable release of the previous repo, please see: [genReads1] (or check out our v2.0 tag).
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Top functions reviewed by kandi - BETA
- Parse the input file .
- Generate random mutations .
- parse a VCF file
- Calculate the sequence errors from the read_data .
- Read a reference sequence
- Writes a BAM record to a BAM file .
- Create a list of the indexes of the reference fasta file .
- Parse a single line .
- Parse the mutation model .
- Run the analysis .
NEAT Key Features
NEAT Examples and Code Snippets
Community Discussions
Trending Discussions on NEAT
QUESTION
How do I set up React Router 6 to restore scroll position when I navigate and when the browser window is refreshed?
React Router 5 has a page about scroll restoration, but I can't find anything about scrolling in the docs for v6, so I guess that you're supposed to handle this yourself with another package. Fair enough, but I can't find anything that's compatible with React Router 6.
The packages react-scroll-restoration and oaf-react-router require v5. (oaf-react-router does list that it supports v6, but the basic usage code example isn't compatible with v6, and the related issue #210 is still open.)
Gatsby and Next.js support scroll restoration out of the box, but I doesn't look like there's a neatly packaged package that you can just use.
This little demo app with server side rendered pages does what I want. Scroll position is restored when navigation back and forth and refreshing the browser window.
Here is the same app using React Router 6, where the scroll position isn't saved and restored, but actually reused between pages. The usual workaround for that is to scroll to the top whenever the page is navigated, but I am not interested in that behaviour.
Edit: React Query writes that the issue with scroll restoration is that pages are refetching data, thereby implying that if the data for rendering the pages is there, scroll restoration just works. I cannot confirm that, because my small React Router 6 app has the issue even without doing any data fetching at all. I feel like there is something small think I am missing in order to get it to work.
Rant: I am quite surprised that the typical answer to this issue is to call window.scrollTo(0, 0) when navigating. This only fixes the issue of the scroll position being transferred between pages. When the scroll position isn't restored, the user experience when navigating between pages is seriously deteriorated. I guess this is partly why pop-up windows have become so popular, but they bring a long suite of other UX issues, so I really want to avoid using them.
ANSWER
Answered 2022-Feb-05 at 16:52Thanks to this comment in oaf-react-router I was able to get it to work with React Router 6. There are a few caveats, though, so I do not consider this a viable solution for a professional web app.
As stated in this code comment,
oaf-react-routerhas to use the same version ofhistoryasreact-router-domdoes. That's whyHistoryRouteris exported asunstable_HistoryRouter. This solution does indeed feel quite unstable.oaf-react-routerdoes not restore the scroll position when refreshing a web page. I don't know if this can be achieved easily, and it's something that might be acceptable.
QUESTION
I'm trying to create a triangular grid with HTML and CSS which involves offsetting each successive triangle in the grid to the left by larger and larger amounts so that each triangle fits neatly next to the previous one. Since the amount that each triangle needs to move is based on it's index in the parent container, I'm currently using JS to set this offset. I'm looking for a way to do this with pure CSS. Using JS like this feels like a hack and I'm wondering if I'm missing something in CSS that would let me access each triangle div's index or perhaps there's another way altogether in CSS to achieve what I'm doing.
...ANSWER
Answered 2022-Mar-16 at 08:16I created the same result with a negative margin. So the triangles don't have to move an increasing space to the left.
QUESTION
Is there a way of joining two dataframes via where a row in the first dataframe is joined with every row in the second dataframe if they share a word in common?
For example:
...ANSWER
Answered 2022-Mar-15 at 18:03With fuzzy_join:
QUESTION
I recently found, that I can make Linux system calls from .NET relatively easy.
For example, to see if I need sudo I just make a signature like this:
ANSWER
Answered 2021-Nov-01 at 11:54So, I was wrong posting the last answer. I found out, the libc binary contained something like __xstat and I called it.
Wrong! As the name would suggest, it was a kind of a private function, something intended to be an implementation detail, not a part of the API.
So I found another function with a normal name: statx. It does exactly what I need, it is well(-ish) documented here:
https://man7.org/linux/man-pages/man2/statx.2.html
Here's the structure and values: https://code.woboq.org/qt5/include/bits/statx.h.html https://code.woboq.org/userspace/glibc/io/fcntl.h.html
TL;DR - it works.
I figured out that -100 (AT_FDCWD) passed as dirfd parameter makes relative paths relative to the current working directory.
I also figured out that passing zeros as flags works (as equivalent to AT_STATX_SYNC_AS_STAT), and the function returns what it should for a regular local filesystem.
So here's the code:
QUESTION
I am working on a project where I am using a shape file to make a choropleth map of the United States. To do this, I downloaded the standard shape file here from the US Census Bureau. After a little bit of cleaning up (there were some extraneous island territories which I removed by changing the plot's axis limits), I was able to get the contiguous states to fit neatly within the bounds of the matplotlib figure. For reference, please see Edit 4 below.
Edit 1: I am using the cb_2018_us_state_500k.zip [3.2 MB] shape file.
The only problem now is that by setting axis limits I now am no longer able to view Alaska and Hawaii (as these are obviously cut out by restricting the axis limits). I would now like to add both of these polygons back in my map but now towards the lower part of the plot figure (the treatment that is given by most other maps of this type) despite its geographical inaccuracy.
To put this more concretely, I am interested in selecting the polygon shapes representing Alaska and Hawaii and moving them to the lower left hand side of my figure. Is this something that would be possible?
I can create a Boolean mask using:
...ANSWER
Answered 2021-Sep-22 at 17:25You could do something like this. You will have to find the right offsets to position Alaska where you want it to be exactly.
Now, you have the following dataframe:
QUESTION
I have a little library where I can define integer types. These are intended for type-safe indexing into arrays and strings in the kind of algorithms I often write. For example, I can use it to define an offset type, Offset and an index type, Idx such that you can get an Offset by subtracting two Idx, you can get Idx by adding or subtracting Offset, but you cannot for example multiple or add Idx.
ANSWER
Answered 2022-Feb-10 at 05:54No, you can't.
By definition of the orphan rules:
Given
impl Trait for T0, animplis valid only if at least one of the following is true:
- Trait is a local trait
- All of
- At least one of the types
T0..=Tnmust be a local type. LetTibe the first such type.- No uncovered type parameters
P1..=Pnmay appear inT0..Ti(excludingTi)Only the appearance of uncovered type parameters is restricted. Note that for the purposes of coherence, fundamental types are special. The T in Box is not considered covered, and Box is considered local.
Local traitA
traitwhich was defined in the current crate. A trait definition is local or not independent of applied type arguments. Giventrait Foo,Foois always local, regardless of the types substituted forTandU.
Local typeA
struct,enum, orunionwhich was defined in the current crate. This is not affected by applied type arguments.struct Foois considered local, butVecis not.LocalTypeis local. Type aliases do not affect locality.
As neither Index nor Range nor Vec are local, and Range is not a fundamental type, you cannot impl Index<...>> for Vec, no matter what you put in the place of the ....
The reason for these rules is that nothing prevents Range or Vec from implementing impl Index> for Vec. Such impl does not exist, and probably never will, but the rules are the same among all types, and in the general case this definitely can happen.
You cannot overload the range operator either - it always creates a Range (or RangeInclusive, RangeFull, etc.).
The only solution I can think about is to create a newtype wrapper for Vec, as suggested in the comments.
If you want your vector to return a wrapped slice, you can use a bit of unsafe code:
QUESTION
async predicate, the "easy" way
One way would be to join_all!() the Futures that compute the filters on every item. And then filters synchronously based on those:
ANSWER
Answered 2022-Feb-03 at 22:46While you can't return an impl Future from an impl FnMut, you can return a boxed future, i.e. a dyn Future which must be boxed because it's in return position. After a bit of borrow checker tetris, we arrive to this:
QUESTION
I am attempting to get IronPDF working on my deployment of an ASP.NET Core 3.1 App Service. I am not using Azure Functions for any of this, just a regular endpoints on an Azure App Service -which, when a user calls it, the service generates and returns a generated PDF document.
When running the endpoint on localhost, it works perfectly- generating the report from the HTML passed into the method. However, once I deploy it to my Azure Web App Service, I am getting a 502 - Bad Gateway error, as attached (displayed in Swagger for neatness sake).
Controller:
...ANSWER
Answered 2021-Dec-14 at 02:19App Service runs your apps in a sandbox and most PDF libraries will fail. Looking at the IronPDF documentation, they say that you can run it in a VM or a container. Since you already are using App Service, simply package your app in a container, publish it to a container registry and configure App Service to run it.
QUESTION
In light of recent malware in existing npm packages, I would like to have a mechanism that lets me do some basic checks before installing new packages or updating existing ones. My main issue are both the packages I install directly, and also the ones I install indirectly.
In general I want to get a list of package-version that npm would install before installing it. More specifically I want the age of the packages that would be installed, so I can generate a warning if any of them is less than a day old.
If I could do that directly with npm, that would be neat, but I'm afraid I need to do some scripting around it.
specific use case:
If I executed npm install react-native-gesture-handler on 2021-10-22 it would have executed the post-install hook of a malicious version of ua-parser and my computer would have been compromised, which is something I would like to avoid.
When I enter npm install react-native-gesture-handler --dry-run, it only tells me which version of react-native-gesture-handler it would have installed, but it would not tell me that it would install a version of ua-parser that was released on that day.
additional notes:
- I know that
npm i --dry-runexists, but it shows only the direct packages. - I know that
npm listexists, but it only shows packages after installing (and thus after install-hooks have already done their harm) - both only show packages version and not their age
- I do not know how I would get a list of packages that would come with a install-hook before installing them
- pointers to alternative ways to deal with malicious npm packages are welcome.
- so far my best solution would be to do "--ignore-scripts" but that would come with it's own set of problems
ANSWER
Answered 2021-Dec-07 at 07:26To find out the malicious package, you will need a script that will check your package for vulnerabilities against national vulnerabilities database
The National Vulnerability Database includes databases of security checklist references, security related software flaws, misconfigurations, product names, and impact metrics.
Mostly all software companies use application security tools like Veracode, Snyk or Checkmarx that does this usually in a stage before deployment in the CICD pipeline.
If you're looking to achieve this locally, you can try
QUESTION
I have this piece of code that reads data from an excel sheet, turns them into objects and then display their details in a neat product card
...ANSWER
Answered 2021-Dec-12 at 19:41You can use localStorage#getItem to get the current list, and JSON#parse to convert it to an array of objects. Then, use Array#push to add the current item, and finally, use localStorage#set and JSON#stringify to save the updated list:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
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Install NEAT
You can use NEAT 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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