bcbb | Incubator for useful bioinformatics code | Genomics library
kandi X-RAY | bcbb Summary
kandi X-RAY | bcbb Summary
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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Top functions reviewed by kandi - BETA
- 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
bcbb Key Features
bcbb Examples and Code Snippets
Lines of Code : 7License : Strong Copyleft (CC BY-SA 4.0)
Copypip install bcbio-gff
python3 -m venv venv
. venv/bin/activate
pip install --upgrade pip
pip install biopython bcbio-gff
Community Discussions
Trending Discussions on bcbb
QUESTION
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 01:19Core 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
QUESTION
I have the following strings:
...ANSWER
Answered 2020-Jul-24 at 03:09Use 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.
QUESTION
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 11:02If 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:
QUESTION
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 09:09You would have to do the contains check on every string in the list:
QUESTION
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 11:56You should do
QUESTION
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 21:12Curious 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:
QUESTION
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 14:47There 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
QUESTION
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 13:33The 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.
QUESTION
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 20:18You 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.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install bcbb
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.
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