gor | tool based on a genomic ordered relational architecture | Genomics library

 by   gorpipe Java Version: v4.5.0 License: AGPL-3.0

kandi X-RAY | gor Summary

kandi X-RAY | gor Summary

gor is a Java library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. gor has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

The GORpipe analysis tool is developed and released by Genuity Science. It originates from the pioneers of population based genomic analysis, deCODE genetics, headquartered in Reykjavik, Iceland. GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using a declarative query language, in a parallel execution engine. It is very efficient in a wide range of use-cases, including genome wide batch analysis, range-queries, genomic table joins of variants and segments, filtering, aggregation etc. The query language combines ideas from SQL and Unix shell pipe syntax, supporting seek-able nested queries, materialized views, and a rich set of commands and functions. For more information see the paper in Bioinformatics (
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            kandi-support Support

              gor has a low active ecosystem.
              It has 34 star(s) with 11 fork(s). There are 8 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 6 open issues and 6 have been closed. On average issues are closed in 24 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of gor is v4.5.0

            kandi-Quality Quality

              gor has no bugs reported.

            kandi-Security Security

              gor has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              gor is licensed under the AGPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              gor releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed gor and discovered the below as its top functions. This is intended to give you an instant insight into gor implemented functionality, and help decide if they suit your requirements.
            • Computes the log likelihood of the permutation
            • Computes the variant likelihood of the counts
            • Find a permutation for an array
            • Convert double array to Double
            • Parse a row
            • Write a single character
            • Writes an integer to the buffer
            • Unzips the input
            • Updates the gradient
            • Iterator
            • Main entry point
            • Execute splits
            • Parses a row
            • Initializes the operation context
            • Runs a script and returns a stream of rows
            • Read header data
            • Compute test statistics
            • Reads the BAM data from the specified input stream
            • Creates a Stream from an input file
            • Create an iterator for the VCF files
            • Returns the list of available blocks
            • Creates the S3 object
            • Returns the optimal indices of two numbers
            • Build a perspective dialog
            • Gets the log likelihood of the permutation
            • Calculates the p - value for the genetic feature
            Get all kandi verified functions for this library.

            gor Key Features

            No Key Features are available at this moment for gor.

            gor Examples and Code Snippets

            Build GORpipe from source
            Javadot img1Lines of Code : 16dot img1License : Non-SPDX (NOASSERTION)
            copy iconCopy
            git clone https://github.com/gorpipe/gor
            
            git submodule update --init --recursive
            
            make build
            
            ./gortools/build/install/gor-scripts/bin/gorpipe "gor tests/data/gor/dbsnp_test.gor | top 10"
            
            Chrom   POS     reference       allele  differentrsIDs
            chr1   
            Setting up Phecode gwas data (Optional)
            Javadot img2Lines of Code : 15dot img2License : Non-SPDX (NOASSERTION)
            copy iconCopy
            https://s3.amazonaws.com/wuxinextcode-sm-public/data/standalone-project-phecode-gwas-data.tar.gz
            
            wget https://s3.amazonaws.com/wuxinextcode-sm-public/data/standalone-project-phecode-gwas-data.tar.gz
            
            tar -xvf standalone-project-phecode-gwas-data.tar  
            Setting up reference data (Optional)
            Javadot img3Lines of Code : 15dot img3License : Non-SPDX (NOASSERTION)
            copy iconCopy
            https://s3.amazonaws.com/wuxinextcode-sm-public/data/standalone-project-data.tar.gz
            
            wget https://s3.amazonaws.com/wuxinextcode-sm-public/data/standalone-project-data.tar.gz
            
            tar -xvf standalone-project-data.tar.gz
            
            ./bin/gorpipe "gor #genes# | top 1  

            Community Discussions

            QUESTION

            Split string by (') and Spaces but keep any space character between two consecutive (')
            Asked 2021-Apr-04 at 23:54

            I need to split a string by (' ') or (''') but if in the string appears ' ' I want to keep only that space. this are examples of the string:

            ...

            ANSWER

            Answered 2021-Apr-04 at 23:54

            Here is some code that does the trick

            Source https://stackoverflow.com/questions/66946076

            QUESTION

            i can't presist data in kubernetes volumes
            Asked 2021-Feb-19 at 10:03

            i have an application that record live traffic and replay them.

            https://github.com/buger/goreplay

            it is a simple app to use, but when i tried to use it with kubernetes i get a problem with persisting data in volumes.

            i want to do this :

            • in pod number one i use the goreplay container and other container that just have a simple python server... the job is the goreplay will listen to the requests coming from outside to the server and save them to a file , this is the deployment file :
            ...

            ANSWER

            Answered 2021-Feb-19 at 10:03

            I replicated it and it looks like the volumes are fine.

            What is not fine, is how you pass file paths to goreplay.

            Here is what I did:

            Source https://stackoverflow.com/questions/66251441

            QUESTION

            How to parse "2021-01-19T16:20:04+0000" as time.Time
            Asked 2021-Jan-19 at 20:00

            I've tried the following format which should catch the +0000 timezone offset as I read https://golang.org/pkg/time/#pkg-constants:

            ...

            ANSWER

            Answered 2021-Jan-19 at 20:00

            What you see is the "default" formatting, e.g. when printed like fmt.Println(ts), which is the result of Time.String(). Quoting from Time.String():

            String returns the time formatted using the format string

            Source https://stackoverflow.com/questions/65797457

            QUESTION

            Why I can't get a pie diagram from dataframe. TypeError: '<' not supported between instances of 'str' and 'int'
            Asked 2021-Jan-01 at 20:26

            I can't get a pie diagram out of the Datafame/ Instead i gor an error TypeError: '<' not supported between instances of 'str' and 'int'

            ...

            ANSWER

            Answered 2021-Jan-01 at 20:17

            Values in column 4 "Quantity" are strings and not numbers. You need to convert those using to_numeric() like you did for column 3

            Source https://stackoverflow.com/questions/65533258

            QUESTION

            Three buttons, three different actions/outputs
            Asked 2020-Oct-30 at 11:28

            This is my first post here and I'm very new to programming. I have this assignment where we are supposed to have three different buttons doing three different things.

            1. The First button is kind of doing what I want. Which is change the text.

            2. The Second button is supposed to open a new activity where it should be a picture. (I've done this assignment before and that worked, but when together with something else it didn't work.)

            3. The Third button is supposed to open a new activity, and there should be a grid view with 6 pictures.

            Here the first XML file and java file. Which after several tries is the easiest (I think) way to start to just make sure I'm able to press the buttons and open the next activity (on button 2 and 3). As you see there are many tries, don't want to delete anything since I'm not sure of what I'm doing. So this is a combo of different tries... Thank you!

            ...

            ANSWER

            Answered 2020-Oct-29 at 11:17

            You almost had it, you just had some basic things wrong, I added comments to help you understand what is going on:

            Source https://stackoverflow.com/questions/64588720

            QUESTION

            C# Using updated array from other method - creating a console game "Nim"
            Asked 2020-Oct-22 at 13:06

            I recently started trying to learn C# (no prior programming experience) and am trying to create a simple mathematical game called "nim"

            I'm far from done but at the moment I'm stuck on an issue I can't seem to solve. I have two methods in the game that control whose turn it is, and how many sticks the user takes away from each pile. the "Game" method is supposed to update the array(which I think it does). but then when it goes back in to the "PlayerTurn" Method, I reset the array because I don't know how to update the value in PlayerTurn using the new updated values in "Game".

            Here's the code: (sorry for it being messy)

            ...

            ANSWER

            Answered 2020-Oct-22 at 13:06

            You have two choices:

            1. Set array in class level - global scope
            2. Pass array as an argument to PlayerTurn method.

            Using 2nd approach:

            Source https://stackoverflow.com/questions/64482804

            QUESTION

            Problem with rendering list item filtered by search query in jQuery
            Asked 2020-Sep-02 at 16:40

            I am making an hotel website as a hobby project but when trying to render the list items depending on the search query by hotels location.

            Initially, I am rendering all hotels which I have stored in an array but when I search by location, let say I type "Stockholm", then I want to show all list items of hotels with location in Stockholm.

            Right now I am only able to hide all list items when typing a location that matches an item.

            Here is my code:

            HTML:

            ...

            ANSWER

            Answered 2020-Sep-02 at 16:40

            You can loop through class i.e :.hotelLocation where location is there .Then , use $(this).text() to match it with the user input and if both are same use .show() to show that li tag .

            Demo code :

            Source https://stackoverflow.com/questions/63708768

            QUESTION

            My AffineTransformation has gaps between pixels
            Asked 2020-Aug-28 at 19:59

            First I want to say that I am not using the AffineTransform class that Oracle made. I am doing my "own" AffineTransform. Why? I am making a pixel engine and I couldn't find any other solution. So I began looking a bit at Wikipedia and how matrices work. I then watched javidx9's video at how to implement it. I got it working. Rotation,reflection,shear etc worked fine but I got a pixel gap. Javidx9 mentioned this in his video and he solved the problem. I tried his solution but I got an "ArrayOutOfIndex error" when doing reflection,rotation and shear. I have been trying to solve the issue but I just can't understand what I am doing due to the complex code. That's why I am here! I need your help!

            I got it working like this (with gaps):

            GIF

            The code I use for the transformation with gaps is the following:

            Render the image with a matrix

            ...

            ANSWER

            Answered 2020-Aug-28 at 18:44

            You are trying to access a pixel that's outside the original image here:

            Source https://stackoverflow.com/questions/63637733

            QUESTION

            How to put Gridview closer to Card widget in Column widget
            Asked 2020-Aug-21 at 10:29

            I'm trying to create a user interface for my app. I need to design like this:

            But my recent UI looks like this:

            In second screenshot I scrolled down because my gridview widget (which has 4 card widgets) doesn't come closer to other widgets. The other widgets are: a widget for titlebar, a card widget which has a graph and subgraph widgets. I put titlebar and graphs card widget inside a stack for showing them above. I put these two combined widgets inside a column with my gridview widget. And I wrap this column widget with a SingleChildScrollView widget because I want my page to be scrollable. So my questions is this: How I can put my gridview widget closer to my card widget as in the first image ?

            Here is the code that I used for this UI:

            ...

            ANSWER

            Answered 2020-Aug-21 at 10:29

            Maybe this happening because of this piece of code in your Stack. This Container take your full screen size. that's why your GridView item build immediate after screen size. Try to remove this Container or reduce the height of it.

            Source https://stackoverflow.com/questions/63519493

            QUESTION

            How to position button in stack
            Asked 2020-Aug-19 at 09:36

            I'm trying to create an UI in flutter recently. I created a stack which has several widgets(graphs, sub-graphs, etc.). The last widget I wanted to show is a raised button. Which must be placed like image below. I used a card widget which has stack with several widgets in it. I put my button in this stack for showing it under the card. But the button must be overflow the card as shown in image below:

            The code I used for card widget:

            ...

            ANSWER

            Answered 2020-Aug-18 at 09:13

            You have to use the position widget inside the stack widget

            A Positioned widget must be a descendant of a Stack, and the path from the Positioned widget to its enclosing Stack must contain only StatelessWidgets or StatefulWidgets (not other kinds of widgets, like RenderObjectWidgets).

            Source https://stackoverflow.com/questions/63464972

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

            Vulnerabilities

            No vulnerabilities reported

            Install gor

            Download the latest release of GORpipe from https://github.com/gorpipe/gor/releases. Extract the package (gor-scripts-<version>.zip).
            Download the latest released GORpipe test data from https://github.com/gorpipe/gor-test-data/releases.
            GORpipe can be invoked and used through an interactive shell session in a terminal - a sort of REPL for GOR, coined GORshell. Start a GORshell by executing:.
            Go to into the gor-scripts folder (gor-scripts-<version>/) and download the reference data found at:. If using a command line, this can be accomplished using wget.
            Go to into the gor-scripts folder (gor-scripts-<version>/) and download the Phecode gwas data found at:. If using a command line, this can be accomplished using wget.
            For developers, to get started with GORpipe, first clone the repo via:.

            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 .
            Find more information at:

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            https://github.com/gorpipe/gor.git

          • CLI

            gh repo clone gorpipe/gor

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            git@github.com:gorpipe/gor.git

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