bcbb | Incubator for useful bioinformatics code | Genomics library

 by   chapmanb Python Version: Current License: No License

kandi X-RAY | bcbb Summary

kandi X-RAY | bcbb Summary

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

Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics. All code, images and documents in this repository are freely available for all uses. Code is available under the MIT license and images, documentations and talks under the Creative Commons No Rights Reserved (CC0) license.
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            kandi-support Support

              bcbb has a low active ecosystem.
              It has 502 star(s) with 220 fork(s). There are 56 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 14 open issues and 58 have been closed. On average issues are closed in 75 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of bcbb is current.

            kandi-Quality Quality

              bcbb has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              bcbb does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              bcbb releases are not available. You will need to build from source code and install.
              Deployable package is available in PyPI.
              bcbb has no build file. You will be need to create the build yourself to build the component from source.

            Top functions reviewed by kandi - BETA

            kandi has reviewed bcbb and discovered the below as its top functions. This is intended to give you an instant insight into bcbb implemented functionality, and help decide if they suit your requirements.
            • Download Setuptools
            • Create fake setuptools package info
            • Build an egg
            • Download setuptools
            • Plots preparation methods for pre - processing
            • Annotate a bar chart
            • Compute the info for a specific variant
            • Download the genome
            • Check if file exists
            • Main function
            • Trim the given adaptor from the given sequence
            • Parse command line arguments
            • Process a single lane
            • Get the number of cores and type of cores
            • Aligns a fastq file
            • Align a BAM file
            • Sort a BAM file
            • Convert two fastq files into a single BAM file
            • Retrieve base inputs for realignment
            • Install a tarball
            • Parse a feature table
            • Produce a report of the metrics
            • Run FreeBayes using FreeBayes
            • Searches for new files
            • Get a program
            • Annotate a nongatk VCF file using a GATKV
            Get all kandi verified functions for this library.

            bcbb Key Features

            No Key Features are available at this moment for bcbb.

            bcbb Examples and Code Snippets

            Module not found error : While module is installed and listed in the pip list
            Pythondot img1Lines of Code : 7dot img1License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            pip install bcbio-gff
            
            python3 -m venv venv
            . venv/bin/activate
            pip install --upgrade pip
            pip install biopython bcbio-gff 
            

            Community Discussions

            QUESTION

            What is the replacement of Microsoft.Web.Services3 in .NET Core that can authenticate with both Username and Signature?
            Asked 2020-Sep-30 at 01:19

            We're currently porting a SOAP client to .NET Core but we're having issues on authentication. Based on our findings, it all boils down to adding both a UsernameToken and Signature to the SOAP Header. In .NET Framework, we authenticate like so:

            ...

            ANSWER

            Answered 2020-Sep-30 at 01:19

            Core does not support the security of the message layer, you can change the security of the message layer to the transport layer or use the .net framework:

            For more information about WCF in core, please refer to this link:

            https://github.com/dotnet/wcf/blob/master/release-notes/SupportedFeatures-v2.1.0.md

            Source https://stackoverflow.com/questions/64129510

            QUESTION

            How to separate text and image path using RegExp?
            Asked 2020-Jul-24 at 08:29

            I have the following strings:

            ...

            ANSWER

            Answered 2020-Jul-24 at 03:09

            Use this RegExp to match the text you don't want:

            [^ ]{20,}

            It matches the unwanted strings because they are the only character sequences that continue on for at least 20 characters without a single space.

            [^ ] means no space. {20,} means repeated at least 20 times.

            Then .split() the entire string using the unwanted text as a delimiter.

            Source https://stackoverflow.com/questions/62408685

            QUESTION

            how to separate the starting text and ending text using sub string in java script?
            Asked 2020-Jun-17 at 11:53

            I have strings that have the text at the start and at the end but in the between there is an image src

            These are the different types of string given below

            ...

            ANSWER

            Answered 2020-Jun-17 at 11:02

            If url is SERVER_UPLOAD_FILE_PATH____::5e2650c2-728c-40af-99a4eb100c432091.png____SERVER_UPLOAD_END click here is the entire string value, I would try this:

            Source https://stackoverflow.com/questions/62414529

            QUESTION

            how to check some static string in python list?
            Asked 2020-Jun-15 at 09:33

            I m checking full string that is exists or not in list

            Here is the code give below for checking the strings in list python

            ...

            ANSWER

            Answered 2020-Jun-15 at 09:09

            You would have to do the contains check on every string in the list:

            Source https://stackoverflow.com/questions/62384845

            QUESTION

            DRF Serializer - How to return field of a foreign key?
            Asked 2019-Jul-30 at 05:51

            Good morning,

            I am really struggling with an issue returning a value from my Django Rest Framework API.

            I have two models, SirTarget & Status. The SirTarget is like a ticket & the Status is a textual status label of the ticket that corresponds to the phase of handling the ticket.

            The models are as follows:

            ...

            ANSWER

            Answered 2019-Apr-29 at 11:56

            QUESTION

            Decode GZIP stream in PHP from C#
            Asked 2019-Feb-18 at 21:12

            I am having some troubles decoding gzip response from an external API. This external API is returning a base64 gziped string back, which I am having problems to decode with PHP.

            This are the response headers from the API:

            ...

            ANSWER

            Answered 2019-Feb-18 at 21:12

            Curious one, I usually look up WordPress core for handling these things, since they got most of edge cases caught over years. Not this one though.

            Rather than trying to rebuild that C# code I have simply brute forced through multiple combinations of related functions and offsets.

            This got it done:

            Source https://stackoverflow.com/questions/54754502

            QUESTION

            Getting user id returned with JWT
            Asked 2019-Feb-07 at 14:47

            Good morning,

            I am writing my first DRF API and am using django-rest-framework-jwt (https://getblimp.github.io/django-rest-framework-jwt/) to handle JWT auth.

            I am using the built in views currently:

            ...

            ANSWER

            Answered 2019-Feb-07 at 14:47

            There are a couple of solutions

            1) First of all the user id is encoded in the JWT, you can decode that in your js yourself.

            2) You can override the payload returned from django-rest-framework-jwt as follows: put the following code for example in your accounts app inside a file called utils.py

            Source https://stackoverflow.com/questions/54575716

            QUESTION

            Not able to deploy a helloworld spring-boot app on Cloud Foundry
            Asked 2018-Aug-13 at 14:35

            Getting following error while deploy a simple helloworld SpringBoot app on Cloud Foundry using cf push helloworld-api command.

            Note: I am not having a manifest.yml file

            Error Log:

            ...

            ANSWER

            Answered 2018-Mar-28 at 13:33

            The output from staging is indicating that all of the detect scripts ran for all of the installed buildpack, including the Java buildpack, but did not detect that any were able to run your app.

            The problem is with your push command, cf push helloworld-api. Since you're deploying a Java app, you need to specify -p path/to/my.jar. You need this so that your compiled application is deployed, not the source code. Without a path, cf push defaults to pushing the current directory which is probably our source code. The Java buildpack only knows how to deploy compiled apps, it cannot build and deploy your source code.

            Source https://stackoverflow.com/questions/49522561

            QUESTION

            Pass PK into model form (not logged in user)
            Asked 2018-Jul-27 at 20:18

            I would like to use a model form on the django.auth user, but I want to be able to pass in the PK to the model to manage other users, not the logged in user.

            Is there a way to do this or do I need to create a regular form?

            Django admin site is not appropriate for my use case.

            Something like (which doesn't work of course...):

            View

            ...

            ANSWER

            Answered 2018-Jul-27 at 20:18

            You just need to get the user you want and then pass it in to the form as the instance argument, exactly as you did with the logged in user.

            Source https://stackoverflow.com/questions/51563248

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

            Vulnerabilities

            No vulnerabilities reported

            Install bcbb

            You can install using 'pip install bcbb' or download it from GitHub, PyPI.
            You can use bcbb 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 .
            Find more information at:

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            CLONE
          • HTTPS

            https://github.com/chapmanb/bcbb.git

          • CLI

            gh repo clone chapmanb/bcbb

          • sshUrl

            git@github.com:chapmanb/bcbb.git

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