gtex-pipeline | GTEx & TOPMed data production and analysis pipelines | BPM library

 by   broadinstitute Python Version: gtex_v8 License: BSD-3-Clause

kandi X-RAY | gtex-pipeline Summary

kandi X-RAY | gtex-pipeline Summary

gtex-pipeline is a Python library typically used in Automation, BPM applications. gtex-pipeline has no vulnerabilities, it has a Permissive License and it has low support. However gtex-pipeline has 1 bugs and it build file is not available. You can download it from GitHub.

GTEx & TOPMed data production and analysis pipelines
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            kandi-support Support

              gtex-pipeline has a low active ecosystem.
              It has 286 star(s) with 164 fork(s). There are 27 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 12 open issues and 60 have been closed. On average issues are closed in 46 days. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of gtex-pipeline is gtex_v8

            kandi-Quality Quality

              gtex-pipeline has 1 bugs (0 blocker, 1 critical, 0 major, 0 minor) and 28 code smells.

            kandi-Security Security

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

            kandi-License License

              gtex-pipeline is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              gtex-pipeline releases are available to install and integrate.
              gtex-pipeline has no build file. You will be need to create the build yourself to build the component from source.
              gtex-pipeline saves you 1035 person hours of effort in developing the same functionality from scratch.
              It has 2348 lines of code, 53 functions and 29 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed gtex-pipeline and discovered the below as its top functions. This is intended to give you an instant insight into gtex-pipeline implemented functionality, and help decide if they suit your requirements.
            • Collapse an annotation
            • Add transcript attributes
            • Subtract a segment
            • Return the union of intervals
            • Apply a patch to a phase VCF file
            • Calculate the presence of missingness
            • Return the DOSage of a gt
            • Parse the mpileup file
            • Remove indels from read_bases
            • Returns a function that parses a tsv file
            • Generate a function that checks file type
            • Pad the value of the b
            • Returns a function that checks file type
            • Prepare a bed dataframe
            • Patch bim ids with indel identifiers
            • Collapse all Strands from a pandas dataframe
            • Load isoform results into pandas DataFrame
            • Get the VCF format from a VCF header
            • Choose a single variant annotation from a CQ string
            • Concatenate a list of files
            • Aggregate rsem results
            • Concatenate reads from a list of read counts
            • Shapeit a VCF file using shapeit
            • Run Torus
            • Prepare expression based on counts
            • Run samtools mpileup
            • Load pair data from a file
            Get all kandi verified functions for this library.

            gtex-pipeline Key Features

            No Key Features are available at this moment for gtex-pipeline.

            gtex-pipeline Examples and Code Snippets

            No Code Snippets are available at this moment for gtex-pipeline.

            Community Discussions

            QUESTION

            Camunda embedded with H2: Cockpit Login fails
            Asked 2022-Mar-09 at 08:50

            I'm currently wokring on a product with the following conditions:

            • Spring-Boot (2.6) with Camunda embedded (7.16)
            • Connection to Camunda configured to use H2 (2.1.210) embedded with the following is configured in application.yml:
            ...

            ANSWER

            Answered 2022-Mar-09 at 08:50

            Remove the "MODE=LEGACY" from the url. Here is a working example:

            https://github.com/rob2universe/vanilla-camunda-template/blob/4625376bf3a5eed9cd1f2853cdf07fe5eca46685/src/main/resources/application.yaml#L17

            Also ensure you use a supported H2 version. That is 1.4.x fro 7.16.x: https://docs.camunda.org/manual/7.16/introduction/supported-environments/

            The BOM will inclcude H2 1.4.200.

            Source https://stackoverflow.com/questions/71391717

            QUESTION

            Plot line from dataframe
            Asked 2022-Mar-04 at 17:04

            I have the following dataframe [1] which contains information relating to music listening. I would like to print a line graph like the following 2 (I got it by putting the data manually) in which the slotID and the average bpm are related, without writing the values by hand . Each segment must be one unit long and must match the average bpm.

            [1]

            ...

            ANSWER

            Answered 2022-Mar-04 at 17:04

            You can loop through the rows and plot each segment like this:

            Source https://stackoverflow.com/questions/71354696

            QUESTION

            Camunda Application not starting up on docker container
            Asked 2022-Feb-27 at 06:01

            I have a simple cammunda spring boot application. which I want to run in a docker container

            I am able to run it locally from IntelliJ but when I try to run it inside a docker it fails with below error message:

            08043 Exception while performing 'Deployment of Process Application camundaApplication' => 'Deployment of process archive 'ct-camunda': The deployment contains definitions with the same key 'ct-camunda' (id attribute), this is not allowed

            docker-compose.yml

            ...

            ANSWER

            Answered 2022-Feb-25 at 11:07

            I don't think this is Docker related. Maybe your build process copies files?

            "The deployment contains definitions with the same key 'ct-camunda' (id attribute), this is not allowed" Check if you have packaged multiple .bpmn files into your deployment. Maybe you accidentally copied the model file in an additional classpath location. You seem to have two deployments with the same id. (This is not about the filename, but the technical id used inside the XML)

            If you are using auto deployment in Spring Boot, you do not have to declare anything in the processes.xml. Use this only in combination with @EnableProcessApplication (or do not use both)

            Source https://stackoverflow.com/questions/71260766

            QUESTION

            Renaming some part of columns of dataframe with values from another dataframe
            Asked 2022-Feb-26 at 12:08

            I want to change the column names from another DataFrame.

            There are some similar questions in stackoverflow, but I need advanced version of it.

            ...

            ANSWER

            Answered 2022-Feb-26 at 12:02

            We could create a mapping from "ID" to "NewID" and use it to modify column names:

            Source https://stackoverflow.com/questions/71276311

            QUESTION

            How to separate Camunda tables to a different schema?
            Asked 2022-Feb-24 at 05:56

            I want to separate Camunda tables to a different schema called camunda but even if I gave the schema-name and table-prefix, it still put all the tables under the public schema.

            Here's my application.yml;

            ...

            ANSWER

            Answered 2022-Feb-24 at 05:56

            Here is a working example for two instance which are using separate database schemas (cam1 and cam2) and not the public schema: https://github.com/rob2universe/two-camunda-instances

            Source https://stackoverflow.com/questions/71219044

            QUESTION

            How to convert json MySQL data into rows and column
            Asked 2022-Feb-23 at 09:26

            I have mysql table like this which contain id and json type column:

            id value 1 {"sys": "20", "dia": "110"} 2 {"bpm": "200"} 3 {"bpm": "123", "sys": "1", "dia": ""}

            Now, I want to have a MySQL query to which data should be as below in which id, val1 will contain keys of the json data and val2 will contain values of respective keys :

            id val1 val2 1 sys 20 1 dia 110 2 bpm 200 3 bpm 123 3 sys 1 3 dia

            Note : I am using MySQL 5.7 version and the keys inside the JSON object are not fixed. It can be any number.

            I want to know how I can achieve this using MySQL query

            Thanks in Advance!!!

            ...

            ANSWER

            Answered 2022-Feb-18 at 12:01

            QUESTION

            Using pyaudio to build a Metronome; wrong timing
            Asked 2022-Feb-08 at 18:29

            So I wanted to build a metronome and decided to use pyaudio. I know there are other ways but I want to make something else later with that.

            Thats my Code so far:

            ...

            ANSWER

            Answered 2022-Feb-08 at 18:16

            You want the play_audio function to be called every 60/bpm seconds, but the function call itself takes time: you need to read the file, open the stream, play the file (who knows how long it is) and close the stream. So that adds to the time from one click to the next.

            To fix this problem, you could try subtracting the time it takes to run the play_audio function from the time you sleep. You could also experiment with running play_audio on a separate thread.

            Source https://stackoverflow.com/questions/71038624

            QUESTION

            Why am I getting "Error processing transaction request: intrinsic gas too low" error when trying to add tUSDT to a particular account?
            Asked 2022-Jan-04 at 18:26

            I am trying to send test USDT to a particular account in Java using the following code:

            ...

            ANSWER

            Answered 2022-Jan-04 at 18:26

            My skills with Ethereum are still not sharp enough to give you a proper answer, but I hope you get some guidance.

            The error states that you are trying to transfer by a party A certain quantity in the name of another party B, to a third one C, but the amount you are trying to transfer, using transferFrom, is greater than the one party B approved party A to send.

            You can check the actual allowance between to parties using the method with the same name of your contract.

            Please, consider review this integration test from the web3j library in Github. It is different than yours but I think it could be helpful.

            Especially, it states that the actual transferFrom operation should be performed by the beneficiary of the allowance. Please, see the relevant code:

            Source https://stackoverflow.com/questions/70483315

            QUESTION

            getting a KeyNotFoundException on a key that appears to exist in a dictionary
            Asked 2021-Dec-25 at 22:29

            full error:

            ...

            ANSWER

            Answered 2021-Dec-25 at 14:11

            From what I can see, in your SongManager you are creating Dictionary ret, but not adding any values to. Instead, you are trying to directly assign values: ret[timings] = notes_enc[name];. Dictionary is not an array, you should use Add() method, like this: ret.Add(timings, notes_enc[name]);

            Source https://stackoverflow.com/questions/70480242

            QUESTION

            Webaudio timing performance
            Asked 2021-Nov-02 at 12:49

            The file below uses ToneJS to play a steam of steady 8th notes. According to the log of the timing, those 8th notes are precisely 0.25 seconds apart.

            However, they don't sound even. The time intervals between the notes are distinctly irregular.

            Why is it so? Is there anything that can be done about it? Or is this a performance limitation of Javascript/webaudio-api? I have tested it in Chrome, Firefox, and Safari, all to the same result.

            Thanks for any information or suggestions about this!

            ...

            ANSWER

            Answered 2021-Nov-02 at 12:49

            For a scheduled triggerAttackRelease, you should pass the time value as the third argument.

            Source https://stackoverflow.com/questions/69804550

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

            Vulnerabilities

            No vulnerabilities reported

            Install gtex-pipeline

            You can download it from GitHub.
            You can use gtex-pipeline 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.

            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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