Jellyfish | A fast multi-threaded k-mer counter | Genomics library
kandi X-RAY | Jellyfish Summary
kandi X-RAY | Jellyfish Summary
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the documentation for details.
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Trending Discussions on Jellyfish
QUESTION
At my job, my team and I (we are five people) use a Java program for everyday work. Rather than require everyone to install Java and run the programs on their laptops, I set up a little VM, put the Java code on that, then built a primitive little webpage as an interface. When a colleague pushes a "RUN CODE" button on the webpage, the webpage runs a simple bash shell script:
...ANSWER
Answered 2022-Mar-06 at 19:38Try:
QUESTION
I am creating a react native app that needs to perform registering and authentication of users. I am able to make a POST request that talks to a mongoose server and saves the information in MongoDB. What I want to do now is that when a user inputs their username, email, and password into a textbox screen in React, I want this informaiton to be savedin my MongoDB database. I am having trouble connecting the frontend (React Native) with the backend (MongoDB database).
Here is the code for my register screen of my React Native App:
...ANSWER
Answered 2022-Feb-27 at 01:40Your front end needs to be making a call to the endpoint, not locally import the code from your backend.
What you're doing with postman is correct. Here is what you need to do in your front end:
QUESTION
Python 3.9.10
notebook==6.4.8
Linux VERSION="22.04 (Jammy Jellyfish)"
I have data including very long UUID strings. Regardless of how many rows or columns are being shown in the Jupyter output, the long UUID strings are being truncated in each individual cell...
I.e.
...ANSWER
Answered 2022-Feb-19 at 19:20To see all the full text, you could use pd.set_option('display.max_colwidth', None)
or if you want to have this for only one display:
QUESTION
I made a Selfbot on Discord (please do not tell me its against the ToS, I have already been told hundreds of times) to send the string "Hello!" everytime someone sends "!hello", and it can also grind other bots such as Dank Memer, all via an on_message() function. But for some reason, when I run the bot, it can login into the account, but the on_message() doesn't seem to work. There is a print() function called in it which is also not displayed, which means that the bot cannot react to the on_message function. It is currently hosted and run on https://replit.com. Please help, I cannot continue developing it after this.
Full Code here:
...ANSWER
Answered 2022-Feb-19 at 16:52Recent Discord API Changes disallows Self-Bots (which is against Discord's ToS) to receive message contents from other users (except itself), hence why your message commands will not work.
QUESTION
I have a list of names and those that are like "John Smith" vs "J Smith" want to pickup.
difflib and .intersection here don’t help, Levenstein too. If it is:
...ANSWER
Answered 2022-Jan-26 at 09:30You can give the following Pythonic implementation a try. No need for fancy levenshtein distance, luckily. In short, split by different words, and then for each potentially matching section check whether:
- The first characters between the two name sections overlap. If not, then there is no match. (e.g.
John
andLucas
,J
andLucas
orJ
andL
) - The two name sections are both longer than 1 character, and are different. If so, then there is no match. (e.g.
Jane
andJohn
)
In the cases where these "no match" requirements don't trigger, then there should be an overlap possible. E.g. J
and Jane
, or Lucas
and Lucas
. I've included extensive comments on how everything works in code, too.
QUESTION
I'm running Python 3.8.10 on WSL2 (Windows Subsystem for Linux) in a corporate environment and am encountering the below error, which I believe is related to pyopenssl / OpenSSL, when attempting to install anything using pip
. It's not clear to me if I made any system-level changes that led to this strange behavior.
ANSWER
Answered 2022-Jan-07 at 17:24From the comments, we ultimately determined that the pip
downloads were being blocked by company policy.
Troubleshooting steps that helped us arrive at the right solution:
A
ping files.pythonhosted.org
was successful, so we next tried ...A manual download of the URI reported by the
pip
error from the original/updated question:
QUESTION
I am writing a Python script to do name matching. For that I want to use the jellyfish module. But when I run this code:
...ANSWER
Answered 2021-Nov-25 at 10:32It's just a warning. You can use the package just fine.
If you don't care to see the warning, you can set up a Python warning filter.
This has been addressed in https://github.com/jamesturk/jellyfish/issues/131 / https://github.com/jamesturk/cjellyfish/pull/12 and will likely be released in the next version of Jellyfish.
QUESTION
I am making a game in pygame where you now swim around and eat small squares, with an animation to the jellyfish. I've made it so you get bigger when eating, but when adding a number between 1-9 to the scale the image sort of gets wider than I want it to become. When I have the scale go up by 10 or more when eating this problem does not occur as badly.
This is the code for the jellyfish/player:
...ANSWER
Answered 2021-Nov-13 at 16:16Pygame behaves weird when using the transformed image repetitively as in case of rotation...
I even have faced crashes due to it
So try using the the same image which is initially loaded as img0,img1,etc. and scale it to the desired size. As of now you were using the same scaled image again and again . This might help
QUESTION
I have compiled CLIPS 6.4 into a shared library (compiled as C++) so that I can use in a C++ application.
I want to now write a simple test C++ application that allows me to:
- Start up the CLIPS engine
- Load a CLIPS program (see animal.clp)
- Assert a fact from the C++ program to the CLIPS engine and receive responses back from CLIPS in my C++ program
- Safely terminate the CLIPS engine and cleanup when nothing on the agenda (all rules fired) - i.e. program completed
ANSWER
Answered 2021-Oct-14 at 20:09The CLIPS Advanced Programming Guide is here: http://clipsrules.sourceforge.net/documentation/v640/apg.pdf
You can use the Load function (section 3.2.2) to load a file. There is an example of its use in section 3.6.1.
You can use the GetNextActivation function (section 12.7.1) to determine if the agenda has any activations.
The simplest way to create facts is using the AssertString function (section 3.3.1). Sections 3.6.2, 4.5.4, and 5.3 have an example use of this function. You can also use the FactBuilder functions described in section 7.1 (with an example in section 7.6.1).
If the results of your program running are represented by facts, you can use the fact query functions via the Eval function to retrieve those values from your program. Section 4.5.4 has an example.
QUESTION
I want to find the similarity between the two strings Example
...ANSWER
Answered 2021-Sep-29 at 13:27You can use a SequenceMatcher
from the built-in module difflib
Code example:
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