gemini | a lightweight db framework for exploring genetic variation
kandi X-RAY | gemini Summary
kandi X-RAY | gemini Summary
The intent of `GEMINI` (GEnome MINIing) is to provide a simple, flexible, and powerful framework for exploring genetic variation for personal and medical genetics. GEMINI is unique in that it integrates genetic variation (from VCF files) with a wealth of genome annotations into a unified database framework. Using this integrated database as the analysis framework, we aim to leverage the expressive power of SQL for data analysis, while attempting to overcome the fundamental challenges associated with using databases for very large (e.g. 1,000,000 variants times 1,000 samples yields one billion genotypes) datasets. In addition, by defining sample relationships with a PED file, GEMINI allows one to explore and test for variants that meet specific inheritance models (e.g., recessive, dominant, etc.).
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Main entry point for the gemini command
- Remove environment variables
- Calculate the mendelian error
- Add command line options to an argument parser
- Install anaconda
- Check gemini dependencies
- Annotate an annotation file
- A context manager for a database connection
- Annotate variants with boolean values
- Generate a list of all possible candidates
- Filter a query
- Get the next record from the result_proxy
- Filters samples
- Filters given query
- Load gemini files
- Prepare samples
- Install the annotation files
- Merge two chunks
- Calculate stats
- Remove PYTHONPATH and PYTHONPATH
- Check gemini requirements
- Run the query
- Update the gemini
- Set the family information
- Load a gemini database
- Create a query to query the results
- Format a GCSV row
- Calculate mendelian error
- Get query
- Retrieve actionable mutations
- Add inheritance arguments to the given parser
- Logarithm of chisq
gemini Key Features
gemini Examples and Code Snippets
Community Discussions
Trending Discussions on gemini
QUESTION
I have a large table with a comments column (contains large strings of text) and a date column on which the comment was posted. I created a separate vector of keywords (we'll call this key) and I want to count how many matches there are for each day. This gets me close, however it counts matches across the entire dataset, where I need it broken down by each day. The code:
...ANSWER
Answered 2021-Apr-21 at 18:50As pointed out in the comments, you can use group_by
from dplyr
to accomplish this.
First, you can extract keywords for each comment/sentence. Then unnest
so each keyword is in a separate row with a date.
Then, use group_by
with both date and comment included (to get frequency for combination of date and keyword together). The use of summarise
with n()
will give number of mentions.
Here's a complete example:
QUESTION
I have made a program using python language which tells your Horoscope. I made that on Jupyter-notebook, Anaconda. I opened it on word its code is: {
...ANSWER
Answered 2021-Mar-18 at 05:38Colab is quite similar to jupyter notebook and is free to use. Just send the link to other once you add your code. https://colab.research.google.com/ is the link. A quick guide is: https://colab.research.google.com/github/jckantor/CBE30338/blob/master/docs/01.01-Getting-Started-with-Python-and-Jupyter-Notebooks.ipynb
QUESTION
I'm writing a Gemini client in Java. Two parts of the Gemini spec are relevant here:
Servers MUST use TLS...
...the strongly RECOMMENDED approach is to implement a lightweight "TOFU" certificate-pinning system which treats self-signed certificates as first-class citizens.
By following this answer How do I accept a self-signed certificate with a Java using SSLSocket I can successfully connect to Gemini servers with self-signed certificates.
But to implement the "TOFU" (trust on first use) requirement I should get hold of the server's certificate to validate that it hasn't changed on subsequent requests. How do I get the certificate?
The code I have is:
...ANSWER
Answered 2021-Mar-08 at 23:26You can store every server certificate and get it afterwords with a custom TrustManager.
An example setup would be:
QUESTION
I need to clean my corpus, it includes these problems
- multiple spaces --> Tables .
- footnote --> 10h 50m,1
- unknown ” --> replace " instead of ” e.g
for instance, you see it here:
...ANSWER
Answered 2021-Feb-23 at 19:43You can use
QUESTION
I was hoping and looking for some other ideas or ways to do this. As you can see, I asked the user for the input which is mmddyyyy (05022001 = May 2, 2001) and used substring in order for me to to take the certain input in the index then parse it. Now, What I want to accomplish is to find another way to do this for example is using the formal date formatter which in my case I didn't use. I think date formatter is alot better than this, but I don't get the idea out of it.
Here's what I've got so far. Thanks in advance.
...ANSWER
Answered 2021-Jan-21 at 17:11You should inform the user of what format you expect.
Take the input string and make a parse attempt. Trap for exception in case of faulty input. No need for you to check the ranges of month and day. LocalDate.parse
makes those data entry validation checks for you.
QUESTION
I am trying to play with the Gemini trading API. I have issued myself an API key and a secret, and after configuring my environment, in which I had a lot of issues setting up and installing requests through pip, I used their example code to create a simple script to read my recent trades. Here is the script, minus my API keys:
...ANSWER
Answered 2021-Jan-11 at 16:10As you are calling an API, there are chances that your API call fails and returns just string or empty response. I would suggest that you first add a check on the status code of your response something like below and then process the json data.
QUESTION
I have this basic exchange monitor script. I'm trying to create one thread per symbol, apart from the main thread which is handling other work, and have them listen to public Gemini websocket endpoints. I'm getting the first thread running and printing exchange data to the console, but not the second one. I had expected to see data from both threads being printed at approximately the same time. I've tried using the threading library instead of asyncio and encountered the same situation.
I realize my two public API MarketWebsocket classes could be combined to be cleaner, I'm still trying to work out a way to easily add other symbols to the list. Thanks for any nudges in the right direction!
...ANSWER
Answered 2021-Jan-03 at 17:22You can do
QUESTION
So, My JS Looks Like This
...ANSWER
Answered 2020-Dec-27 at 20:18If you want to get a string with the names of the genres, you could use .map()
and .join()
. Use .map()
to turn the array into an array of genre names, from an array of objects. Then use .join()
to combine the array into a string.
QUESTION
I am using Derby 10.8.2 which requires Gemini DBAcess. These versions are very old (circa 2011) and do not work with JRE > 1.8.
As the title asks, does anyone know of a more recent version that will work in an OSGi evnironment?
Thanks
...ANSWER
Answered 2020-Dec-11 at 03:29The Derby community have an open Enhancement Request to support OSGi on the most recent versions of Derby: DERBY-7056
There are a set of proposed changes to provide this support.
My understanding is that the primary blocker on this is access to somebody who is relatively familiar with OSGi and could test the support, as none of the Derby committers are users of OSGi.
So perhaps you could volunteer to work with the Derby community and help get the OSGi support tested and committed?
QUESTION
I've made this bot to reply to tweets; it's detecting and registering the users id but it doesn't tweet at them and i don't know why.
What could it be?
I've deleted the token and keys from the code
the code should reply with one of the strings randomly from the listtt
ANSWER
Answered 2020-Nov-17 at 07:58Did you change App permissons to "Read, Write, and Direct Messages" in Settings of your project? And after that you must regenerate keys and tokens.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install gemini
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