hail | Cloud-native genomic dataframes and batch computing | Genomics library

 by   hail-is Python Version: 0.2.126 License: MIT

kandi X-RAY | hail Summary

kandi X-RAY | hail Summary

hail is a Python library typically used in Artificial Intelligence, Genomics, Spark applications. hail has no bugs, it has no vulnerabilities, it has a Permissive License and it has medium support. However hail build file is not available. You can install using 'pip install hail' or download it from GitHub, PyPI.

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.

            kandi-support Support

              hail has a medium active ecosystem.
              It has 881 star(s) with 228 fork(s). There are 59 watchers for this library.
              There were 9 major release(s) in the last 6 months.
              There are 33 open issues and 2042 have been closed. On average issues are closed in 42 days. There are 55 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of hail is 0.2.126

            kandi-Quality Quality

              hail has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              hail 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

              hail releases are available to install and integrate.
              Deployable package is available in PyPI.
              hail has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              It has 209126 lines of code, 19650 functions and 1482 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

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

            hail Key Features

            No Key Features are available at this moment for hail.

            hail Examples and Code Snippets

            df.fillna() not working when updating multiple columns from a slice
            Pythondot img1Lines of Code : 8dot img1License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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] 
            copy iconCopy
            from django.contrib import admin
            from django.urls import include, path
            urlpatterns = [
                path('admin/', admin.site.urls),
                path('', include('imagem.urls', namespace='home')),
            Replace particular string patter in a string python
            Pythondot img3Lines of Code : 11dot img3License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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)
            Python 3x : Parse an xml file with namespaces using python xml.etree
            Pythondot img4Lines of Code : 20dot img4License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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',
            os.getenv returns empty output - python
            Pythondot img5Lines of Code : 3dot img5License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            os.putenv('SPARK_HOME', '/opt/spark')
            os.putenv('HAIL_HOME', '/opt/hail/hail')
            my code for remove @user and punctuation does not work
            Pythondot img6Lines of Code : 3dot img6License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            names = re.compile('@[A-Za-z0-9_]+')
            string = re.sub(names, '@USER', input_string)
            Explanding GeoPandas Multipolygon Dataframe To One Poly Per Line
            Pythondot img7Lines of Code : 18dot img7License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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
            Finding the x-y coordinate
            Pythondot img8Lines of Code : 6dot img8License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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 ...
            KeyError why is this happening I have all keys present(python)?
            Pythondot img9Lines of Code : 4dot img9License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            FINAL_DICT[word] = tuple(d[word] for d in FINAL_SOL)
            FINAL_DICT[word] = tuple(FINAL_DICT[word] for d in FINAL_SOL)
            Making a table in matplotlib
            Pythondot img10Lines of Code : 27dot img10License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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


            Importing images from public folder in react
            Asked 2022-Apr-15 at 08:22

            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.



            Answered 2022-Apr-15 at 08:22

            change the src from /public/images to /images

            Source https://stackoverflow.com/questions/71881492


            iterate over columns to count words in a sentence and put it in a new column
            Asked 2022-Apr-08 at 04:54

            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:



            Answered 2022-Apr-08 at 04:54

            Use across() to apply the same function to multiple columns:

            Source https://stackoverflow.com/questions/71790948


            Referencing Non-Decision/Non-Optimization Variables in AnyLogic MultiObjective Optimization
            Asked 2022-Jan-22 at 05:50

            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).



            Answered 2021-Oct-26 at 22:32

            Unfortunately, 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:

            1. create a Map> extraVars outside evaluate
            2. then populate extraVars inside evaluate method before call to engine.stop() using solution.getIteration as key

            Source https://stackoverflow.com/questions/69730053


            Fix for SQL UPDATE: updating all the rows to the same value instead of basing value on another table column
            Asked 2022-Jan-06 at 23:55

            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):



            Answered 2022-Jan-06 at 22:42

            You 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:

            Source https://stackoverflow.com/questions/70611983


            Capacitor 3 and Ionic 6 Android build hitting "uses-sdk:minSdkVersion 1 cannot be smaller than version 21 declared in library [:capacitor-app]"
            Asked 2021-Dec-29 at 21:32

            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:



            Answered 2021-Dec-29 at 21:32

            First 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!).

            1. Delete android folder from the Ionic Project's root folder.
            2. run command ionic capacitor add android
            3. run command ionic capacitor build android
            4. Build & run!

            Source https://stackoverflow.com/questions/70465495


            image as circle background (d3.js svg)
            Asked 2021-Dec-08 at 15:40

            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.



            Answered 2021-Dec-08 at 12:15

            I've used your code to assemble a small example, which you can see below.

            1. Inside svg > defs, create one pattern per node and use that pattern (with the ID of the company) to fetch the logo of that company;
            2. Reference the pattern for the node using the information you already have.

            Some pointers on your code:

            1. 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!) than d3.map;
            2. 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;
            3. 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.

            Source https://stackoverflow.com/questions/70264049


            Jackson ObjectMapper JSON to Java Object RETURNS NULL Values
            Asked 2021-Dec-05 at 14:08

            I'm trying to loop through the child object of a JSON array which stores objects. My JSON file is as follows:



            Answered 2021-Dec-05 at 14:08

            You are missing a class that matches the list of Species that your JSON contains:

            Source https://stackoverflow.com/questions/70222096


            What is causing a csv load error in weka?
            Asked 2021-Nov-16 at 07:33

            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?



            Answered 2021-Nov-16 at 07:33

            Weka'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.

            Source https://stackoverflow.com/questions/69983402


            Does Apache Spark 3 support GPU usage for Spark RDDs?
            Asked 2021-Sep-23 at 05:53

            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?



            Answered 2021-Sep-23 at 05:53

            As 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++.

            Source https://stackoverflow.com/questions/69273205


            php json array of arrays and get some key values from deep nested
            Asked 2021-Sep-04 at 11:12

            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.



            Answered 2021-Sep-04 at 11:12

            First of all, you should convert your JSON to array then use loop(foreach, for, while...) and get value accordingly like this:

            Source https://stackoverflow.com/questions/69054587

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


            No vulnerabilities reported

            Install hail

            You can install using 'pip install hail' or download it from GitHub, PyPI.
            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.


            Hail has been widely adopted in academia and industry, including as the analysis platform for the genome aggregation database and UK Biobank rapid GWAS. Learn more about Hail-powered science.
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            pip install hail

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            gh repo clone hail-is/hail

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