gemini | a lightweight db framework for exploring genetic variation

 by   arq5x Python Version: v0.6.2 License: MIT

kandi X-RAY | gemini Summary

kandi X-RAY | gemini Summary

gemini is a Python library. gemini has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can download it from GitHub.

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.).
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            kandi-support Support

              gemini has a highly active ecosystem.
              It has 282 star(s) with 116 fork(s). There are 46 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 165 open issues and 396 have been closed. On average issues are closed in 165 days. There are 3 open pull requests and 0 closed requests.
              OutlinedDot
              It has a negative sentiment in the developer community.
              The latest version of gemini is v0.6.2

            kandi-Quality Quality

              gemini has 0 bugs and 0 code smells.

            kandi-Security Security

              gemini has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              gemini code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              gemini is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              gemini releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions are available. Examples and code snippets are not available.
              gemini saves you 6221 person hours of effort in developing the same functionality from scratch.
              It has 12959 lines of code, 399 functions and 72 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed gemini and discovered the below as its top functions. This is intended to give you an instant insight into gemini implemented functionality, and help decide if they suit your requirements.
            • 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
            Get all kandi verified functions for this library.

            gemini Key Features

            No Key Features are available at this moment for gemini.

            gemini Examples and Code Snippets

            No Code Snippets are available at this moment for gemini.

            Community Discussions

            QUESTION

            How to colSum grouped by date
            Asked 2021-Apr-21 at 18:50

            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 18:50

            As 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:

            Source https://stackoverflow.com/questions/67197493

            QUESTION

            How can I run my python code on google and give access to public or other users without using any money
            Asked 2021-Mar-18 at 05:45

            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 05:38

            Colab 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

            Source https://stackoverflow.com/questions/66685325

            QUESTION

            How can I get hold of the server's certificate at run time when opening an SSLSocket in a Java client?
            Asked 2021-Mar-08 at 23:26

            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 23:26

            You can store every server certificate and get it afterwords with a custom TrustManager.

            An example setup would be:

            Source https://stackoverflow.com/questions/66519707

            QUESTION

            preprocessing the text and excluding form footnotes , extra spaces and
            Asked 2021-Feb-23 at 19:43

            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 19:43

            QUESTION

            Is there other way of getting an input like date format?
            Asked 2021-Jan-21 at 17:11

            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 17:11

            You 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.

            Source https://stackoverflow.com/questions/65831738

            QUESTION

            Simple JSON Decode Error in Gemini API Started Out of Nowhere
            Asked 2021-Jan-11 at 16:10

            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 16:10

            As 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.

            Source https://stackoverflow.com/questions/65670364

            QUESTION

            Trying to understand how to use multithreaded websockets in Python but seem to be stuck with one thread
            Asked 2021-Jan-03 at 17:22

            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 17:22

            QUESTION

            nodejs axios JSON with Objects under the same name
            Asked 2020-Dec-27 at 20:18

            So, My JS Looks Like This

            ...

            ANSWER

            Answered 2020-Dec-27 at 20:18

            If 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.

            Source https://stackoverflow.com/questions/65470014

            QUESTION

            Is there a recent version of Apache Derby that is supported in OSGi?
            Asked 2020-Dec-11 at 03:29

            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 03:29

            The 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?

            Source https://stackoverflow.com/questions/65228245

            QUESTION

            Not being able to answer tweets with twitter bot
            Asked 2020-Nov-17 at 07:58

            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 07:58

            Did you change App permissons to "Read, Write, and Direct Messages" in Settings of your project? And after that you must regenerate keys and tokens.

            Source https://stackoverflow.com/questions/64868095

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install gemini

            Install ``GEMINI`` using the automated installation script, gemini_install.py. This script installs GEMINI along with required python libraries, third party tools and data files used for variant annotation. The installation documentation contains additional details on installed files and tools.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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