asap | scalable bacterial genome assembly , annotation | Genomics library
kandi X-RAY | asap Summary
kandi X-RAY | asap Summary
ASA³P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates. ASA³P is a fully automatic, locally executable and scalable assembly, annotation and higher-level analysis pipeline creating results in standard bioinformatics file formats as well as sophisticated HTML5 documents. Its main purpose is the automatic processing of NGS WGS data of multiple closely related isolates, thus transforming raw reads into assembled and annotated genomes and finally gathering as much information on every single bacterial genome as possible. Per-isolate analyses are complemented by comparative insights. Therefore, the pipeline incorporates many best-in-class open source bioinformatics tools and thus minimizes the burden of ever-repeating tasks. Envisaged as a preprocessing tool it provides comprehensive insights as well as a general overview and comparison of analysed genomes along with all necessary result files for subsequent deeper analyses. All results are presented via modern HTML5 documents comprising interactive visualizations.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of asap
asap Key Features
asap Examples and Code Snippets
Lines of Code : 88License : Strong Copyleft (GPL-3.0)
Copyproject-dir
├── reports (HTML5 reports)
│ ├── index.html
$ login: asap-test
$ password: asap-test
project-dir
├── [state.running | state.finished | state.failed]
├── asap.log (global logging file)
├── config.xls (config spreadsheet)
├── con $ sudo docker pull oschwengers/asap
$ wget https://zenodo.org/record/3780003/files/asap.tar.gz
$ tar -xzf asap.tar.gz
$ rm asap.tar.gz
$ #/asap-docker.sh -p [-s ] [-a ASAP_DIR] [-z] [-c] [-d]
$ asap/asap-docker.sh -p example-lmonocytogenes -s /tmp
project-dir
├── config.xls
├── data
│ ├── reference-genome-1.gbk
│ ├── reference-genome-2.fasta
│ ├── isolate-1-1.fastq.gz
│ ├── isolate-1-2.fastq.gz
│ ├── isolate-2-1.fastq.gz
│ ├── isolate-2-2.fastq.gz
│ ├── isolate-3.1.bax.h5
│ ├── Community Discussions
Trending Discussions on asap
QUESTION
I have a repo with a env/ folder. This folder is for personal configurations, but, the file must not be changed in the repo. (i.e: you introduce database data (hosts, ports, passwords), but you don't want the repo to have that info.)
Note, the file has other info as well, so the file must be in the repo. (so no .gitignore)
How can I exclude the file changes when pushing to the origin?
So far, I've been deleting and then adding again the extra info every time I make a push. So I need to change the workflow asap.
Also, the repo is not mine, so I can't add or change much around.
...ANSWER
Answered 2021-Jun-09 at 23:45For this there is the update-index command.
Most likely you want something like this:
QUESTION
USE VHT_RPT
SELECT
[QueueName] AS QueueName, Interval,
CONVERT(VARCHAR(20), Interval, 103) AS DATEPART,
CONVERT(VARCHAR(20), Interval, 108) AS TIMEPART,
COUNT(CALLID) AS Callbacks
FROM
(SELECT
[QueueName] AS QueueName,
DATEADD(MINUTE, DATEDIFF(HOUR, '1970-01-01', InTimestart) * 60 + FLOOR(DATEPART(MINUTE, InTimeStart) / 15) * 15, '1970-01-01') AS Interval,
CALLID
FROM
QDump
WHERE
InResult IN ('I2', -- ASAP callback
'I5', -- Scheduled callback
'I8', -- Web ASAP Callback
'I9', -- Web scheduled callback
'I18', -- Second Chance callback
'I25', -- After Hours scheduled callback
'I32', -- Virtual Queue ASAP callback
'I33' -- Date Book scheduled callback))
AS Sub,
WHERE
interval BETWEEN '05/03/2021' AND '05/08/2021' -- Date Format is "MM-DD-YYYY"
GROUP BY
Interval, [QueueName]
ORDER BY
Interval
ANSWER
Answered 2021-May-28 at 03:19It is simple ->
QUESTION
I am trying to read a log file which has key value pair separated by colon (:), but for some key value is having lines and space between. I have to read the DETAILED_DESC : till the end of the file. What would the appropriate way to read.
...ANSWER
Answered 2021-May-25 at 11:41If the line starts always with DETAILED_DESC : you can simply do
QUESTION
I am creating "say" command for my bot and it is fine, But when I tag someone in-between content it does not send the remaining message.
For Example:
!say [user mention] take your role asap
but the output is:
[user mention]
Code:
...ANSWER
Answered 2021-May-15 at 07:52That's because you seperate arguments by spaces. To make argument that has space inside it simply put * inside of the async def audit(ctx, msg=None): like that:
QUESTION
Having made a program which streams PNG images to the browser by means of a multipart/x-mixed-replace Content-Type header, I noticed that only the frame before-last is displayed in the tag, as opposed to the most recently sent one.
This behaviour is very annoying, as I'm only sending updates when the image changes to save on bandwidth, which means that the wrong frame will be on screen while I'm waiting for it to update.
Specifically, I am using Brave Browser (based on chromium), but as I have tried with both "shields" up and down, I assume this problem occurs also in other chromium-based browsers at least.
Searching for the problem yields only one relevant result (and many non-relevant ones) which is this HowToForge thread, with no replies. Likewise, I also thought the issue is to do with buffering, but I made sure to flush the buffer to no avail, much alike to the user in the thread. The user does report that it works on one of their servers though and not the other, which then lead me to believe that it may be to do with a specific HTTP header or something along those lines. My first guess was Content-Length because the browser can tell when the image is complete from that, but it didn't seem to have any effect.
So essentially, my question is: Is there a way to tell the browser to show the most recent multipart/x-mixed-replace and not the one before? And, if this isn't standard behaviour, what could the cause be?
And of course, here's the relevant source code, though I imagine this is more of a general HTTP question than one to do with the code:
Server ...ANSWER
Answered 2021-Jan-06 at 23:04A part inside a multipart MIME message starts with the MIME header and ends with the boundary. There is a single boundary before the first real part. This initial boundary closes the MIME preamble.
Your code instead assumes that a part starts with the boundary. Based on this assumption you first send the boundary, then the MIME header and then the MIME body. Then you stop sending until the next part is ready. Because of this the end of one part will only be detected once you send the next part, since only then you send the end boundary of the previous part.
To fix this your code should initially send one boundary to end the MIME preamble. For each new part it should then send the MIME header, the MIME body and then the boundary to end this part.
QUESTION
Our desktop ERP built in VB.NET is suddenly not showing scrollbars in DataGrid control on Windows 10 after updates - KB5001337, KB5001406 (May 2021)
The space for the scrollbars appears but there are no up and down arrows visible!
Same application is showing the scrollbars in Datagrid control on Windows 7 PCs/ windows 10 without these updates. We have multiple Datagrid controls throughout the application so need to find a fix asap
Windows.forms.Datagrid .NET Framework version 3 was used to build in VS 2010
Have already tried -
- Settings -> Ease of Access-> Automatically hide scrollbars in Windows (turn off)
- Tried running the ERP using Windows 7 compatibility mode
ANSWER
Answered 2021-Apr-20 at 11:17Yeah I was too facing this issue. I have just uninstalled this update
QUESTION
I have a Java servlet that generates some arbitrary report file and returns it as a download to the user's browser. The file is written directly to the servlet's output stream, so if it is very large then it can successfully download in chunks. However, sometimes the resulting data is not large enough to get split into chunks, and either the client connection times out, or it runs successfully but the download doesn't appear in the browser's UI until it's 100% done.
This is what my servlet code looks like:
...ANSWER
Answered 2021-May-04 at 20:44Well, it looks like shrinking the size of my output buffer with response.setBufferSize(1000); allowed my stress test file to download successfully. I still don't know why response.flushBuffer() didn't seem to do anything, but at least as long as I generate data quickly enough to fill that buffer size before timing out, the download will complete.
QUESTION
Considering I have the following code:
...ANSWER
Answered 2021-Apr-18 at 09:23As I know RxJS tends to standalone schedulers usage. And it works as expected:
QUESTION
So, I have the following scenario.
I am working on a system for academical papers. I have several inputs that are for stuff like author name, coauthors, title, type of paper, introduction, objectives and so on. I store all that information in a database. The user has a Preview button which when clicked, generates a Word asynchronously and sends the file location back to the user and that file is afterwards shown to the user in an iframe using Google Doc Viewer.
There's a specific use case where the user/author of the paper can attach a .docx file with a table, or a .jpeg file for a figure. That table/figure has to be included inside the final .docx file.
For the .docx generation process I am using PHPWord.
So up until this point everything works fine, but my issues start when I try to mix everything and put together the .docx file.
Approach Number One
My first approach on doing this was to do everything with PHPWord. I create the file, add the texts where required and in the case of the image just insert the image and after that the figure caption below the image.
Things get tricky though, when I try doing the same thing with the .docx table file. My only option was to get the table XML using this. It did the trick, but the problem I ran into was that when I opened the resulting Word file, the table was there, but had lost all of its styling and had transparent borders. Because of those transparent borders, afterwards when converting it to PDF the borders were ignored and the table info is just scrambled text.
Approach Number Two (current one)
After fighting with Approach Number One and just complicating stuff more, I decided to do something different. Since I already generated one docx file with the main paper information and I needed to add another docx file, I decided to use the DocX Merge Library.
So, what i basically did was I have three generated word files, one for the main paper information, one for the table and one for the table caption (that last one is mainly to not overcomplicated the order of information). Also, that data is not in the table .docx file.
Then I run this:
...ANSWER
Answered 2021-Apr-17 at 14:33After a lot of attempts to fix it, I wasn't able to achieve what I wanted with PHPWord and the merging library I mentioned.
Since I needed to fix this I decided to invest in the paid library I mentioned in my question. It was an expensive purchase, but for those who are interested, it does exactly what was required and it does it perfectly.
The two main functions I required were document merging and importing of content to a .docx file.
So I had to purchase the Premium package. Once there, the library literally does everything for you.
Example for docx files merge code:
QUESTION
As the title says, I am having some trouble with AVAssetWriter and memory.
Some notes about my environment/requirements:
- I am NOT using ARC, but if there is a way to simply use it and get it all working I'm all for it. My attempts have not made any difference though. And the environment I will be using this in requires memory to be minimised / released ASAP.
- Objective-C is a requirement
- Memory usage must be as low as possible, the 300mb it takes up now is unstable when testing on my device (iPhone X).
This is the code used when taking the screenshots below https://gist.github.com/jontelang/8f01b895321d761cbb8cda9d7a5be3bd
The problem / items kept around in memoryMost of the things that seem to take up a lot of memory throughout the processing seems to be allocated in the beginning.
So at this point it doesn't seem to me that the issues are with my code. The code that I personally have control over seems to not be an issue, namely loading the images, creating the buffer, releasing it all seems to not be where the memory has a problem. For example if I mark in Instruments the majority of the time after the one above, the memory is stable and none of the memory is kept around.
The only reason for the persistent 5mb is that it is deallocated just after the marking period ends.
Now what?I actually started writing this question with the focus being on wether my code was releasing things correctly or not, but now it seems like that is fine. So what are my options now?
- Is there something I can configure within the current code to make the memory requirements smaller?
- Is there simply something wrong with my setup of the writer/input?
- Do I need to use a totally different way of making a video to be able to make this work?
In the documentation of CVPixelBufferCreate Apple states:
If you need to create and release a number of pixel buffers, you should instead use a pixel buffer pool (see CVPixelBufferPool) for efficient reuse of pixel buffer memory.
I have tried with this as well, but I saw no changes in the memory usage. Changing the attributes for the pool didn't seem to have any effect as well, so there is a small possibility that I am not actually using it 100% properly, although from comparing to code online it seems like I am, at least. And the output file works.
The code for that, is here https://gist.github.com/jontelang/41a702d831afd9f9ceeb0f9f5365de03
And here is a slightly different version where I set up the pool in a slightly different way https://gist.github.com/jontelang/c0351337bd496a6c7e0c94293adf881f.
Update 1So I looked a bit deeper into a trace, to figure out when/where the majority of the allocations are coming from. Here is an annotated image of that:
The takeaway is:
- The space is not allocated "with" the AVAssetWriter
- The 500mb that is held until the end is allocated within 500ms after the processing starts
- It seems that it is done internally in AVAssetWriter
I have the .trace file uploaded here: https://www.dropbox.com/sh/f3tf0gw8gamu924/AAACrAbleYzbyeoCbC9FQLR6a?dl=0
...ANSWER
Answered 2021-Apr-04 at 15:33When creating Dispatch Queue, ensure you create a queue with Autorlease Pool. Replace
DISPATCH_QUEUE_SERIALwithDISPATCH_QUEUE_SERIAL_WITH_AUTORELEASE_POOL.Wrap each iteration of
forloop into autorelease pool as well
like this:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install asap
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
