gor | tool based on a genomic ordered relational architecture | Genomics library
kandi X-RAY | gor Summary
kandi X-RAY | gor Summary
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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Top functions reviewed by kandi - BETA
- 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
gor Key Features
gor Examples and Code Snippets
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
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
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
Trending Discussions on gor
QUESTION
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 23:54Here is some code that does the trick
QUESTION
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 10:03I 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:
QUESTION
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 20:00What 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
QUESTION
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 20:17Values in column 4 "Quantity" are strings and not numbers. You need to convert those using to_numeric()
like you did for column 3
QUESTION
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.
The First button is kind of doing what I want. Which is change the text.
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.)
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 11:17You almost had it, you just had some basic things wrong, I added comments to help you understand what is going on:
QUESTION
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 13:06You have two choices:
- Set array in class level - global scope
- Pass array as an argument to PlayerTurn method.
Using 2nd approach:
QUESTION
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 16:40You 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 :
QUESTION
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):
The code I use for the transformation with gaps is the following:
Render the image with a matrix
...ANSWER
Answered 2020-Aug-28 at 18:44You are trying to access a pixel that's outside the original image here:
QUESTION
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 10:29Maybe 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.
QUESTION
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 09:13You 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).
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install gor
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:.
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