hail | Cloud-native genomic dataframes and batch computing | Genomics library
kandi X-RAY | hail Summary
kandi X-RAY | hail Summary
Hail is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data. Hail is built to scale and has first-class support for multi-dimensional structured data, like the genomic data in a genome-wide association study (GWAS). Hail is exposed as a Python library, using primitives for distributed queries and linear algebra implemented in Scala, Spark, and increasingly C++. See the documentation for more info on using Hail.
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Top functions reviewed by kandi - BETA
- Compute an ld - score table .
- Create batch jobs .
- Define a de -ovo table .
- Annotate a dataset .
- Build a table of PC_Relate .
- Calculate the logistic regression rows .
- The King function .
- Imports a table .
- Register the function .
- Test the logistic regression table .
hail Key Features
hail Examples and Code Snippets
garage_cat_columns = ['GarageType','GarageYrBlt','GarageQual','GarageCond','GarageFinish']
no_garage = testing.loc[testing[garage_cat_columns].isnull().all(axis=1), 'Id'].tolist()
testing.loc[df['Id'].isin(no_garage), garage_cat_columns]
from django.contrib import admin
from django.urls import include, path
urlpatterns = [
path('admin/', admin.site.urls),
path('', include('imagem.urls', namespace='home')),
]
project_name/project_name/se
import re
sentence = '\U0001f308 \U0001f64b The dark clouds disperse the hail subsides and one neon lit rainbow with a faint second arches across the length of the A \u2026'
matches = re.findall('[\u0001\U00010000-\U0001FFFF]', sentence)
results = root.findall('exist:result', ns)
import xml.etree.ElementTree as et
data = "" # As specified in question.
root = et.fromstring(data)
ns = {'exist':'http://exist.sourceforge.net/NS/exist',
'niwa':'
os.putenv('SPARK_HOME', '/opt/spark')
os.putenv('HAIL_HOME', '/opt/hail/hail')
names = re.compile('@[A-Za-z0-9_]+')
string = re.sub(names, '@USER', input_string)
exploded = original_df.explode()
Explode muti-part geometries into multiple single geometries.
Each row containing a multi-part geometry will be split into
multiple rows with single geometries, thereby
for row_number, row in enumerate(rows):
final_word = next((word for word in words if word in row), None)
if final_word:
print(f"{final_word} right")
^ YOU ARE HERE ...
FINAL_DICT[word] = tuple(d[word] for d in FINAL_SOL)
FINAL_DICT[word] = tuple(FINAL_DICT[word] for d in FINAL_SOL)
columns = ('year','Freeze', 'Wind', 'Flood', 'Quake', 'Hail')
rows = ['%d year' % x for x in (100, 50, 20, 10, 5)]
# Get some pastel shades for the colors
colors = plt.cm.BuPu(np.linspace(0, 0.5, len(rows)))
n_rows = len(data)
# Initia
Community Discussions
Trending Discussions on hail
QUESTION
OK last hail mary here. I've seen this question a lot but no clear answer. I moved all of my images out of my src
folder to my public
folder into a sub-folder images
. And used the URL like ./images/my-image.png
but the image isn't populating. I am using create-react-app. How do I call images from a public
folder outside of my src
folder.
ANSWER
Answered 2022-Apr-15 at 08:22change the src from /public/images
to /images
QUESTION
I have some columns titles essay 0-9, I want to iterate over them count the words and then make a new column with the number of words. so essay0 will get a column essay0_num with 5 if that is how many words it has in it.
so far i got cupid <- cupid %>% mutate(essay9_num = sapply(strsplit(essay9, " "), length))
to count the words and add a column but i don't want to do it one by one for all 10.
i tried a for loop:
...ANSWER
Answered 2022-Apr-08 at 04:54Use across()
to apply the same function to multiple columns:
QUESTION
TLDR: Looking to pull values of non-decision variables from OptQuest solution or find an viable work around for obtaining this information.
I'm currently running a weighted multi-objective optimization (custom) experiment in AnyLogic that deals with the profit of a manufacturer, distributor and retailer in a distribution channel. My decision variables are the reorder points (r) and the reorder quantities (Q) for each of these members. My objectives are the profit of the channel (root.MultObjs) and the profit of the retailer (root.RObj).
...ANSWER
Answered 2021-Oct-26 at 22:32Unfortunately, there is no easy way to get COptQuestSolution
to carry extra variables. The way I have done this before is by saving extra information before root
object is destroyed. To do it:
- create a
Map> extraVars
outsideevaluate
- then populate
extraVars
insideevaluate
method before call toengine.stop()
usingsolution.getIteration
as key
QUESTION
I have the following query to combine the columns into a comma-separated list (using this because STRING_AGG
does not work for me probably due to an older version of SQL Server which I do not have control over):
ANSWER
Answered 2022-Jan-06 at 22:42You need to reference and alias the sheldus51_copy table in a FROM clause at the top level, so that both the UPDATE and the nested select (correlated subquery) can reference the same rows. Try:
QUESTION
I'm quite stuck here despite having found a few quite similar Stack Overflow questions.
My specific case is trying to get an app to build on Android which I recently updated to Ionic 6 and most notably added Capacitor – while still using Cordova for a couple of plugins, but no longer for builds.
The work in progress is public on this branch.
The build error I get is:
...ANSWER
Answered 2021-Dec-29 at 21:32First Solition
In Android Studio, Select File > Project Structure
.
In that window, on the left side, select the app
module.
Once selected, click on the Flavors
tab on the top of the window pane.
Set your minimum SDK version to 21.
Explanation: As Android updates to new versions, tools that developers use for Android change (& update or deprecate). Because of this, you cannot use new tools on an old version. Version 1
is the very first Android SDK (and we definitely don't want to be using that!). Capacitor requires the SDK be at least version 21
.
Second Solution
If that doesn't work, we can always try rebuilding the android app all together. (Note: By doing this, you will lose any custom changes in the AndroidManifest.xml, a custom app icon, etc. If you haven't touched any of these things, then great!).
- Delete
android
folder from the Ionic Project's root folder. - run command
ionic capacitor add android
- run command
ionic capacitor build android
- Build & run!
QUESTION
UPDATED I have made a force directed graph using D3.js. Each node corresponds to a company, and each link corresponds how they are related to each other according to the link color. What I would like to achieve is to use the image URLs within "nodes" data and show a different image for each bubble. Currently I was able to set a fixed static/identical image for all of my bubbles. I tried to connect the pattern to my "nodes" data, but unsuccessfully which ended up in an infinite loop.
Simple HTML canvas for my svg and two buttons for the zoom in and zoom out by click.
...ANSWER
Answered 2021-Dec-08 at 12:15I've used your code to assemble a small example, which you can see below.
- Inside
svg > defs
, create onepattern
per node and use thatpattern
(with the ID of the company) to fetch the logo of that company; - Reference the
pattern
for the node using the information you already have.
Some pointers on your code:
- You already use ES6 logic, so you can also use
Array.prototype.map
and other functions. They're generally much more readable (and natively implemented!) thand3.map
; - There is no need to keep so many arrays of values, generally having fewer sources of truth for your data will make the code simpler to maintain and update in the future;
- Use clear variable names! LS and LT are logical when you know the context, but when you revisit this code in 6 months you might not instantly know what you were talking about when you wrote it.
QUESTION
I'm trying to loop through the child object of a JSON array which stores objects. My JSON file is as follows:
...ANSWER
Answered 2021-Dec-05 at 14:08You are missing a class that matches the list of Species
that your JSON contains:
QUESTION
Im receiving the following error when trying to open a CSV file in Weka version 3.8.5
File not recognized as an 'CSV data files' file Reason: wrong number of values. Read 2, expected 12, read Token [EOL], Line 2 Problem encountered on Line:2
I have read solutions to similar errors on this site and can't seem to find what is wrong with my particular file. However, as a very newbie weka user, it may just be my misunderstanding of the issue. Can someone take a look at the sample csv data below and let me know if you see what I am not understnding or missing?
...ANSWER
Answered 2021-Nov-16 at 07:33Weka's CSVLoader cannot handle rows that span multiple lines (despite quoting). Once all your rows (header and data) are one per line, you should be fine.
The common-csv (unofficial) Weka package should be able to handle rows spanning multiple lines.
QUESTION
I am currently trying to run genomic analyses pipelines using Hail(library for genomics analyses written in python and Scala). Recently, Apache Spark 3 was released and it supported GPU usage.
I tried spark-rapids library start an on-premise slurm cluster with gpu nodes. I was able to initialise the cluster. However, when I tried running hail tasks, the executors keep getting killed.
On querying in Hail forum, I got the response that
That’s a GPU code generator for Spark-SQL, and Hail doesn’t use any Spark-SQL interfaces, only the RDD interfaces.
So, does Spark3 not support GPU usage for RDD interfaces?
...ANSWER
Answered 2021-Sep-23 at 05:53As of now, spark-rapids doesn't support GPU usage for RDD interfaces.
Source: Link
Apache Spark 3.0+ lets users provide a plugin that can replace the backend for SQL and DataFrame operations. This requires no API changes from the user. The plugin will replace SQL operations it supports with GPU accelerated versions. If an operation is not supported it will fall back to using the Spark CPU version. Note that the plugin cannot accelerate operations that manipulate RDDs directly.
Here, an answer from spark-rapids team
Source: Link
We do not support running the RDD API on GPUs at this time. We only support the SQL/Dataframe API, and even then only a subset of the operators. This is because we are translating individual Catalyst operators into GPU enabled equivalent operators. I would love to be able to support the RDD API, but that would require us to be able to take arbitrary java, scala, and python code and run it on the GPU. We are investigating ways to try to accomplish some of this, but right now it is very difficult to do. That is especially true for libraries like Hail, which use python as an API, but the data analysis is done in C/C++.
QUESTION
I have a JSON data get from an API and I want to get/access for each AttributeValues the code
and values
to store into the tables, code as tables columns and values are dynamic for each record. I don't need to store the Attachements and Total from the json values.
i want to store to tables as an insert into (ID, TrackingNumber, CustomerFull) values (json values). any codeigniter, or php soluton or hint will be much appricate.
ANSWER
Answered 2021-Sep-04 at 11:12First of all, you should convert your JSON to array then use loop(foreach, for, while...) and get value accordingly like this:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install hail
You can use hail like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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